OK, I've been bashing my head against this for another couple of hours and I've eliminated a whole bunch of possible causes. There no longer seems to be any issues with assemblies or references, I'm now simply getting an error in the aspnet_complier task. This is the output when I try to build the Web Deployment project:

Target "AspNetCompiler" in file "C:\Program Files\MSBuild\Microsoft\WebDeployment\v8.0\Microsoft.WebDeployment.targets":
  Using "AspNetCompiler" task from assembly "Microsoft.Build.Tasks, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a".
  Task "AspNetCompiler"
   
    Command:
    C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\aspnet_compiler.exe -v /mick.admin.justsuper.roadhouse.com.au -p "C:\Inetpub\Just Super Admin" -u -f -d "C:\Documents and Settings\mick\My Documents\Visual Studio 2005\Projects\mick.admin.justsuper.roadhouse.com.au\Deploy\Debug\\"
    The "AspNetCompiler" task is using "aspnet_compiler.exe" from "C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\aspnet_compiler.exe".
    Utility to precompile an ASP.NET application
    Copyright (C) Microsoft Corporation. All rights reserved.
   
    c:\Inetpub\Just Super Admin\App_Code\DataAccess\DB.cs(16): warning CS0436: The type 'Roadhouse.CMS.Library.Config' in 'c:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\Temporary ASP.NET Files\mick.admin.justsuper.roadhouse.com.au\caae5859\e614d45a\App_Code.0.cs' conflicts with the imported type 'Roadhouse.CMS.Library.Config' in 'c:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\Temporary ASP.NET Files\mick.admin.justsuper.roadhouse.com.au\caae5859\e614d45a\assembly\dl3\44604d1d\e0ef643b_a4a0c601\Roadhouse.CMS.Library.DLL'. Using the one in 'c:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\Temporary ASP.NET Files\mick.admin.justsuper.roadhouse.com.au\caae5859\e614d45a\App_Code.0.cs'.
    c:\Inetpub\Just Super Admin\App_Code\Config.cs(47): warning CS0618: 'System.Configuration.ConfigurationSettings.AppSettings' is obsolete: 'This method is obsolete, it has been replaced by System.Configuration!System.Configuration.ConfigurationManager.AppSettings'
    c:\Inetpub\Just Super Admin\App_Code\Config.cs(52): warning CS0618: 'System.Configuration.ConfigurationSettings.GetConfig(string)' is obsolete: 'This method is obsolete, it has been replaced by System.Configuration!System.Configuration.ConfigurationManager.GetSection'
    c:\Inetpub\Just Super Admin\App_Code\Config.cs(56): warning CS0618: 'System.Configuration.ConfigurationSettings.GetConfig(string)' is obsolete: 'This method is obsolete, it has been replaced by System.Configuration!System.Configuration.ConfigurationManager.GetSection'
    c:\Inetpub\Just Super Admin\Forms\FormBuilder\UpdateDatabase.aspx.cs(41): warning CS0618: 'System.Configuration.ConfigurationSettings.AppSettings' is obsolete: 'This method is obsolete, it has been replaced by System.Configuration!System.Configuration.ConfigurationManager.AppSettings'
    c:\Inetpub\Just Super Admin\Forms\FormBuilder\GetDbSchema.aspx.cs(37): warning CS0618: 'System.Configuration.ConfigurationSettings.AppSettings' is obsolete: 'This method is obsolete, it has been replaced by System.Configuration!System.Configuration.ConfigurationManager.AppSettings'
    c:\Inetpub\Just Super Admin\Forms\UserControls\Form.ascx.cs(63): warning CS0618: 'System.Web.UI.WebControls.Xml.Document' is obsolete: 'The recommended alternative is the XPathNavigator property. Create a System.Xml.XPath.XPathDocument and call CreateNavigator() to create an XPathNavigator. http://go.microsoft.com/fwlink/?linkid=14202'
    c:\Inetpub\Just Super Admin\Forms\UserControls\Form.ascx.cs(334): warning CS0618: 'System.Configuration.ConfigurationSettings.AppSettings' is obsolete: 'This method is obsolete, it has been replaced by System.Configuration!System.Configuration.ConfigurationManager.AppSettings'
    c:\Inetpub\Just Super Admin\Forms\UserControls\Form.ascx.cs(36): warning CS0414: The private field 'Cms.FormBuilder.Form.bHasXML' is assigned but its value is never used
    ASPNETCOMPILER : error ASPRUNTIME: Object reference not set to an instance of an object.
    The command exited with code 1.
   
  Done executing task "AspNetCompiler" -- FAILED.
Done building target "AspNetCompiler" in project "Deploy.wdproj" -- FAILED.

Done building project "Deploy.wdproj" -- FAILED.