Mikhail,
The HTML markup is still all over the shop, this afternoon I started manually reconfiguring it to look like it should and have noted just now when I went back in that the HTML that I reformatted is okay and displays as it should. So it looks like I will have to complete this step and manually reformat the rest of my aspx file.
The Atlas/Ajax assemblies are reference through the Global cache with a reference added to each page for the AJAX Toolkit.
On a brighter note I just ran the Edit/Advanced/Format Document option and the whole document has been reformatted correctly and the HTML tags have been corrected (changed to lower case). So everything is honk dory now.. Thanks for your help, persistance, and assistance.
Regards..
Peter.