I'd backup the database and all the files right now, whatever state they are in.

then, I would get the new version 3.1.0 (http://www.dotnetnuke.com/default.aspx?tabid=125) and unzip those files over it. This version doesn't have a web.config so that you don't overwrite it. It has a release.config. Copy this file and rename the copy to be web.config (you'll have to delete your old one, but you have it backed up, right?)

post any errors here.

sorry about the huge post

Thanks alot guys, I've totally backed everything up now, but I'm reluctant to overwrite the whole site, is this the only way to get to the bottom of this.

Bear in mind it was working perfectly, then I backed up web.config and changed the original. Site errored out, so I just replaced the modified web.config with the backed up copy.

The error messages I get change each time I hit refresh...

for example:

Configuration Error

Line 256:                <add assembly="System.EnterpriseServices, Version=1.0.5000.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a"/>
Line 257:                <add assembly="System.Web.Mobile, Version=1.0.5000.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a"/>
Line 258:                <add assembly="*"/>
Line 259:            </assemblies>
Line 260:

=== Pre-bind state information ===
LOG: DisplayName = EfficionConsulting.Articles
 (Partial)
LOG: Appbase = file:///E:/HSSD Intranet/DotNetNuke
LOG: Initial PrivatePath = bin
Calling assembly : (Unknown).
===

LOG: Policy not being applied to reference at this time (private, custom, partial, or location-based assembly bind).
LOG: Post-policy reference: EfficionConsulting.Articles
LOG: Attempting download of new URL file:///C:/WINDOWS/Microsoft.NET/Framework/v1.1.4322/Temporary ASP.NET Files/root/28dd00a3/e661e034/EfficionConsulting.Articles.DLL.
LOG: Attempting download of new URL file:///C:/WINDOWS/Microsoft.NET/Framework/v1.1.4322/Temporary ASP.NET Files/root/28dd00a3/e661e034/EfficionConsulting.Articles/EfficionConsulting.Articles.DLL.
LOG: Attempting download of new URL file:///E:/HSSD Intranet/DotNetNuke/bin/EfficionConsulting.Articles.DLL.
LOG: Policy not being applied to reference at this time (private, custom, partial, or location-based assembly bind).
LOG: Post-policy reference: EfficionConsulting.Articles, Version=3.1.5.31394, Culture=neutral, PublicKeyToken=null

Line 256:                <add assembly="System.EnterpriseServices, Version=1.0.5000.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a"/>
Line 257:                <add assembly="System.Web.Mobile, Version=1.0.5000.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a"/>
Line 258:                <add assembly="*"/>
Line 259:            </assemblies>
Line 260:

=== Pre-bind state information ===
LOG: DisplayName = EfficionConsulting.Articles
 (Partial)
LOG: Appbase = file:///E:/HSSD Intranet/DotNetNuke
LOG: Initial PrivatePath = bin
Calling assembly : (Unknown).
===

LOG: Policy not being applied to reference at this time (private, custom, partial, or location-based assembly bind).
LOG: Post-policy reference: EfficionConsulting.Articles
LOG: Attempting download of new URL file:///C:/WINDOWS/Microsoft.NET/Framework/v1.1.4322/Temporary ASP.NET Files/root/28dd00a3/e661e034/EfficionConsulting.Articles.DLL.
LOG: Attempting download of new URL file:///C:/WINDOWS/Microsoft.NET/Framework/v1.1.4322/Temporary ASP.NET Files/root/28dd00a3/e661e034/EfficionConsulting.Articles/EfficionConsulting.Articles.DLL.
LOG: Attempting download of new URL file:///E:/HSSD Intranet/DotNetNuke/bin/EfficionConsulting.Articles.DLL.
LOG: Policy not being applied to reference at this time (private, custom, partial, or location-based assembly bind).
LOG: Post-policy reference: EfficionConsulting.Articles, Version=3.1.5.31394, Culture=neutral, PublicKeyToken=null

My Web.config file...

<configuration>
  <!-- register local configuration handlers -->
  <configSections>
    <sectionGroup name="dotnetnuke">
      <section name="data" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="logging" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="scheduling" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="htmlEditor" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="searchIndex" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="searchDataStore" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="friendlyUrl" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
    </sectionGroup>
    <sectionGroup name="memberrolesprototype">
      <section name="membership" type="Microsoft.ScalableHosting.Configuration.MembershipConfigHandler, MemberRole, Version=1.0.0.0, Culture=neutral, PublicKeyToken=b7c773fb104e7562" />
      <section name="roleManager" type="Microsoft.ScalableHosting.Configuration.RolesConfigHandler, MemberRole, Version=1.0.0.0, Culture=neutral, PublicKeyToken=b7c773fb104e7562" />
      <section name="profile" type="Microsoft.ScalableHosting.Configuration.ProfileConfigHandler, MemberRole, Version=1.0.0.0, Culture=neutral, PublicKeyToken=b7c773fb104e7562" />
      <section name="anonymousIdentification" type="Microsoft.ScalableHosting.Configuration.AnonymousIdConfigHandler, MemberRole, Version=1.0.0.0, Culture=neutral, PublicKeyToken=b7c773fb104e7562" />
    </sectionGroup>
  </configSections>
  <!-- the old connectionString setting has been deprecated and replaced with the data provider section below -->
  <appSettings>
    <add key="SiteSqlServer" value="Server=(local);Database=INTRANET;Integrated Security=SSPI;" />
    <add key="MachineValidationKey" value="FC5FDE4D46C417168661164E3BF123CA35122A9C" />
    <add key="MachineDecryptionKey" value="62D0FF623119588E5F15A9145D897A580D50C831800EA42F" />
    <add key="MachineValidationMode" value="SHA1" />
    <add key="InstallTemplate" value="DotNetNuke.install.resources" />
    <add key="AutoUpgrade" value="true" />
    <add key="UseDnnConfig" value="true" />
    <add key="ShowMissingKeys" value="false" />
    <!-- Show missing translation keys (for development use) -->
    <add key="InstallationDate" value="4/12/2005" />
  </appSettings>
  <system.web>
    <!-- HttpModules for Common Functionality -->
    <httpModules>
      <add name="UrlRewrite" type="DotNetNuke.HttpModules.UrlRewriteModule, DotNetNuke.HttpModules.UrlRewrite" />
      <add name="Exception" type="DotNetNuke.HttpModules.ExceptionModule, DotNetNuke.HttpModules.Exception" />
      <add name="UsersOnline" type="DotNetNuke.HttpModules.UsersOnlineModule, DotNetNuke.HttpModules.UsersOnline" />
      <add name="ProfilePrototype" type="Microsoft.ScalableHosting.Profile.ProfileModule, MemberRole, Version=1.0.0.0, Culture=neutral, PublicKeyToken=b7c773fb104e7562" />
      <add name="AnonymousIdentificationPrototype" type="Microsoft.ScalableHosting.Security.AnonymousIdentificationModule, MemberRole, Version=1.0.0.0, Culture=neutral, PublicKeyToken=b7c773fb104e7562" />
      <add name="RoleManagerPrototype" type="Microsoft.ScalableHosting.Security.RoleManagerModule, MemberRole, Version=1.0.0.0, Culture=neutral, PublicKeyToken=b7c773fb104e7562" />
      <add name="DNNMembership" type="DotNetNuke.HttpModules.DNNMembershipModule, DotNetNuke.HttpModules.DNNMembership" />
      <add name="Personalization" type="DotNetNuke.HttpModules.PersonalizationModule, DotNetNuke.HttpModules.Personalization" />
    </httpModules>
    <!-- This is for FTB 3.0 support -->
    <httpHandlers>
      <add verb="GET" path="FtbWebResource.axd" type="FreeTextBoxControls.AssemblyResourceHandler, FreeTextBox" />
    </httpHandlers>
    <!-- set code access security trust level - this is generally set in the machine.config
  <trust level="Medium" originUrl="http://localhost/.*" />
  -->
    <!-- set debugmode to false for running application -->
    <compilation debug="false" />
    <!-- permits errors to be displayed for remote clients -->
    <customErrors mode="Off" />
    <!-- Forms or Windows authentication -->
    <authentication mode="Forms">
      <forms name=".DOTNETNUKE" protection="All" timeout="60" />
    </authentication>
    <!--
      <identity impersonate="true"/>
      <authentication mode="Windows">
      </authentication>
  -->
    <!-- allow large file uploads -->
    <httpRuntime useFullyQualifiedRedirectUrl="true" maxRequestLength="8192" />
    <!--  GLOBALIZATION
  This section sets the globalization settings of the application.
  Utf-8 is not supported on Netscape 4.x
  If you need netscape compatiblity leave iso-8859-1.
  UTF-8 is recommended for complex languages
  -->
    <globalization culture="en-US" uiCulture="en" requestEncoding="UTF-8" responseEncoding="UTF-8" fileEncoding="UTF-8" />
    <!--<globalization culture="en-US" uiCulture="en"  fileEncoding="iso-8859-1" requestEncoding="iso-8859-1" responseEncoding="iso-8859-1"/>-->
    <!-- page level options -->
    <pages validateRequest="false" enableViewStateMac="true" />
  </system.web>
  <memberrolesprototype>
    <!-- membership config:
              Attributes:
                  userIsOnlineTimeWindow="int"                Time window (in minutes) to consider a User as being Online after since last activity
                  hashAlgorithmType="[SHA1|SHA512|MD5|...]"   Any valid hash algorithm supported by .NET framework, default is SHA1
              Child nodes:
                <providers>              Providers (class must inherit from MembershipProvider)
                    <add                 Add a provider
                        name="string"    Name to identify this provider instance by
                        type="string"    Class that implements MembershipProvider
                        provider-specific-configuration />

                </providers>

                Configuration for SqlMembershipProvider and AccessMembershipProvider:
                   connectionStringName="string"              Name corresponding to the entry in <connectionStrings> section where the connection string for the provider is specified
                   passwordAttemptThreshold="int"             The number of failed password attempts, or failed password answer attempts that are allowed before locking out a user?s account
                   passwordAttemptWindow="int"                The time window, in minutes, during which failed password attempts and failed password answer attempts are tracked
                   enablePasswordRetrieval="[true|false]"     Should the provider support password retrievals
                   enablePasswordReset="[true|false]"         Should the provider support password resets
                   requiresQuestionAndAnswer="[true|false]"   Should the provider require Q & A
       minRequiredPasswordLength="int"        The minimum password length
       minRequiredNonalphanumericCharacters="int" The minimum number of non-alphanumeric characters
                   applicationName="string"                   Optional string to identity the application: defaults to Application Metabase path
                   requiresUniqueEmail="[true|false]"         Should the provider require a unique email to be specified
                   passwordFormat="[Clear|Hashed|Encrypted]"  Storage format for the password: Hashed (SHA1), Clear or Encrypted (Triple-DES)
                   description="string"                       Description of what the provider does
        -->
    <membership userIsOnlineTimeWindow="15">
      <providers>
        <add name="DNNSQLMembershipProvider" type="DotNetNuke.Security.Membership.DNNSQLMembershipProvider, DNNSQLMembershipProvider" connectionStringName="SiteSqlServer" enablePasswordRetrieval="true" enablePasswordReset="true" requiresQuestionAndAnswer="false" minRequiredPasswordLength="4" minRequiredNonalphanumericCharacters="0" requiresUniqueEmail="false" passwordFormat="Encrypted" applicationName="/" description="Stores and retrieves membership data from the local Microsoft SQL Server database" />
      </providers>
    </membership>
    <!-- Configuration for roleManager:
                enabled="[true|false]"                            Feature is enabled?
                cacheRolesInCookie="[true|false]"                 Cache roles in cookie?
                cookieName=".ASPXROLES"                           Cookie Name
                createPersistentCookie="[true|false]"             Creates a persistent cookie or session cookie?
                cookieTimeout="30"                                Cookie Timeout
                cookiePath="/"                                    Cookie Path
                cookieRequireSSL="[true|false]"                   Set Secure bit in Cookie
                cookieSlidingExpiration="[true|false]"            Reissue expiring cookies?
                cookieProtection="[None|Validation|Encryption|All]"    How to protect cookies from being read/tampered
                defaultProvider="string"                          Name of provider to use by default
                domain="[domain]"                                 Enables output of the "domain" cookie attribute set to the specified value
                maxCachedResults="int"                            Maximum number of roles to cache in cookie

               Child nodes:
                <providers>              Providers (class must inherit from RoleProvider)

                    <add                 Add a provider
                        name="string"    Name to identify this provider instance by
                        type="string"    Class that implements RoleProvider
                        provider-specific-configuration />

                </providers>

                <providers> type="TypeName"                        Class that inherits from System.Web.Security.RoleProvider
                    providerSpecificConfig                        Config for the provider

           Configuration for SqlRoleProvider:
                   connectionStringName="string"  Name corresponding to the entry in <connectionStrings> section where the connection string for the provider is specified
                   description="string"           Description of what the provider does
                   commandTimeout="int"           Command timeout value for SQL command
        -->
    <roleManager cacheRolesInCookie="true" cookieName=".ASPXROLES" cookieTimeout="30" cookiePath="/" cookieRequireSSL="false" cookieSlidingExpiration="true" createPersistentCookie="false" cookieProtection="All">
      <providers>
        <add name="DNNSQLRoleProvider" type="DotNetNuke.Security.Role.DNNSQLRoleProvider, DNNSQLRoleProvider" connectionStringName="SiteSqlServer" applicationName="/" description="Stores and retrieves roles data from the local Microsoft SQL Server database" />
      </providers>
    </roleManager>
    <!--
            Configuration for profile:
             <profile>
                enabled="[true|false]"   Feature is enabled?
                automaticSaveEnabled="[true|false]" Enable automatic save of profile
                inherits="type-name"     Class from which the profile type inherits from. This type must inherit from ProfileBase type.

                <providers>              Providers (class must inherit from ProfileProvider)
                    <add                 Add a provider (only single entry supported)
                        name="string"    Name to identify this provider instance by
                        type="string"    Class that implements ProfileProvider
                        provider-specific-configuration />
                <providers>

                <properties>                Optional element. List of properties in the Profile system
                    <add                    Add a property
                            name="string"                 Name of the property
                            type="string"                 Optional. Type of the property. Default: string.
                            readOnly="[true|false]"       Optional. Is Value read-only. Default: false.
                            defaultValue="string"         Optional. Default Value. Default: Empty string.
                            allowAnonymous="[true|false]" Optional. Allow storing values for anonymous users. Default: false.
                            serializeAs=["String|Xml|Binary|ProviderSpecific"] Optional. How to serialize the type. Default: ProviderSpecific.
                        />
                </properties>
             </profile>
        -->
    <profile enabled="true">
      <providers>
        <add name="AspNetSqlProvider" type="DotNetNuke.Users.Profile.DNNSQLProfileProvider, DNNSQLProfileProvider" connectionStringName="SiteSqlServer" applicationName="/" description="Stores and retrieves profile data from the local Microsoft SQL Server database" />
      </providers>
      <properties>
        <add name="FirstName" type="string" allowAnonymous="true" />
        <add name="LastName" type="string" allowAnonymous="true" />
        <add name="Unit" type="string" allowAnonymous="true" />
        <add name="Street" type="string" allowAnonymous="true" />
        <add name="City" type="string" allowAnonymous="true" />
        <add name="Region" type="string" allowAnonymous="true" />
        <add name="PostalCode" type="string" allowAnonymous="true" />
        <add name="Country" type="string" allowAnonymous="true" />
        <add name="Telephone" type="string" allowAnonymous="true" />
        <add name="Fax" type="string" allowAnonymous="true" />
        <add name="Cell" type="string" allowAnonymous="true" />
        <add name="Website" type="string" allowAnonymous="true" />
        <add name="IM" type="string" allowAnonymous="true" />
        <add name="TimeZone" type="integer" allowAnonymous="true" />
        <add name="PreferredLocale" type="string" allowAnonymous="true" />
      </properties>
    </profile>
    <!--
            anonymousIdentification configuration:
                enabled="[true|false]"                            Feature is enabled?
                cookieName=".ASPXANONYMOUS"                       Cookie Name
                cookieTimeout="100000"                            Cookie Timeout in minutes
                cookiePath="/"                                    Cookie Path
                cookieRequireSSL="[true|false]"                   Set Secure bit in Cookie
                cookieSlidingExpiration="[true|false]"            Reissue expiring cookies?
                cookieProtection="[None|Validation|Encryption|All]"    How to protect cookies from being read/tampered
                domain="[domain]"                                 Enables output of the "domain" cookie attribute set to the specified value
        -->
    <anonymousIdentification enabled="true" cookieName=".ASPXANONYMOUS" cookieTimeout="100000" cookiePath="/" cookieRequireSSL="false" cookieSlidingExpiration="true" cookieProtection="None" domain="" />
  </memberrolesprototype>
  <dotnetnuke>
    <htmlEditor defaultProvider="Ftb3HtmlEditorProvider">
      <providers>
        <clear />
        <!--
         FTB options:
         ============
         toolbarStyle="Office2003|OfficeXP|Office2000|OfficeMac"  Sets the default FTB Toolbar style
         enableProFeatures="[true|false]"                         Pro features require a license from FreeTextBox
                                                                  or you may test them with localhost only
         spellCheck="[{none}|IeSpellCheck|NetSpell]"              IeSpellCheck is free for non-commercial use only
                                                                  NetSpell requires some integration work
    -->
        <add name="Ftb3HtmlEditorProvider" type="DotNetNuke.HtmlEditor.Ftb3HtmlEditorProvider, DotNetNuke.Ftb3HtmlEditorProvider" providerPath="~\Providers\HtmlEditorProviders\Ftb3HtmlEditorProvider\" toolbarStyle="Office2003" enableProFeatures="false" spellCheck="" />
      </providers>
    </htmlEditor>
    <searchIndex defaultProvider="ModuleIndexProvider">
      <providers>
        <clear />
        <add name="ModuleIndexProvider" type="DotNetNuke.Services.Search.ModuleIndexer, DotNetNuke.Search.Index" providerPath="~\Providers\SearchProviders\ModuleIndexer\" />
      </providers>
    </searchIndex>
    <searchDataStore defaultProvider="SearchDataStoreProvider">
      <providers>
        <clear />
        <add name="SearchDataStoreProvider" type="DotNetNuke.Services.Search.SearchDataStore, DotNetNuke.Search.DataStore" providerPath="~\Providers\SearchProviders\SearchDataStore\" />
      </providers>
    </searchDataStore>
    <data defaultProvider="SqlDataProvider">
      <providers>
        <clear />
        <add name="SqlDataProvider" type="DotNetNuke.Data.SqlDataProvider, DotNetNuke.SqlDataProvider" connectionStringName="SiteSqlServer" upgradeConnectionString="" providerPath="~\Providers\DataProviders\SqlDataProvider\" objectQualifier="" databaseOwner="dbo" />
      </providers>
    </data>
    <logging defaultProvider="XMLLoggingProvider">
      <providers>
        <clear />
        <add name="XMLLoggingProvider" type="DotNetNuke.Services.Log.EventLog.XMLLoggingProvider, DotNetNuke.XMLLoggingProvider" configfilename="LogConfig.xml.resources" providerPath="~\Providers\LoggingProviders\XMLLoggingProvider\" />
      </providers>
    </logging>
    <scheduling defaultProvider="DNNScheduler">
      <providers>
        <clear />
        <add name="DNNScheduler" type="DotNetNuke.Services.Scheduling.DNNScheduling.DNNScheduler, DotNetNuke.DNNScheduler" providerPath="~\Providers\SchedulingProviders\DNNScheduler\" debug="false" maxThreads="1" />
      </providers>
    </scheduling>
    <friendlyUrl defaultProvider="DNNFriendlyUrl">
      <providers>
        <clear />
        <add name="DNNFriendlyUrl" type="DotNetNuke.Services.Url.FriendlyUrl.DNNFriendlyUrlProvider, DotNetNuke.HttpModules.UrlRewrite" />
      </providers>
    </friendlyUrl>
  </dotnetnuke>
</configuration>

DeveloperMCDBA I took your advice exactly, but with the new version I'm still getting the same errors. I changed the siteSQL string to match my DB, but the errors seem to relate to something else.

Could this be something to do with IIS, the fact that I created and then deleted a Virtual Directory as a subfolder of the DNN VDir?