Build Fails for VS 2008 whenever i am using Framework 2.0 Code

Question

I used a code from 'instant results for ASP.NET 2.0' from IMAR Spa.... of WROX and modified the code using VS 2005 and then build it was very good for me but recently got the attack of folder virus. So I was to remove my VS 2005 and Upgraded the system as well. Later on I installed VS 2008 and copied whole of the code in to a VS 2008 Project from VS 2005 code base and modified the code as per my needs and published as well. But as per the requirements Earlier this month on 1 OCT 2011, I upgraded My VS 2008 with SP1 build from Microsoft since then i am getting build failed error and also no able to trace any errors in it. To remove this i again removed whole of the windows Installation and get on with initial IDE but still I am getting the same error. Could you please tell me if the last publish on previous windows with SP1 had wrote in my Settings files or did any others changes in my code which is causing build failed with out any errors. because i have used the same code always to build. I cannot revert the changes as my code contains more then 1200 folders and more then 100000 files and is more then 300 MB in size. i have used Jquery, Javascript, Vb.net files, cs.net files, Sitemaps, DB's, etc in my website. Please could any one help me debugging and publishing my website.
Thanks