File Not Found error is one of those errors that will keep you awake for days. You checked the event log but there was no error message to provide you with any insight on why SharePoint could not find a file, and yet did not report any specific error either in the event log or the Sharepoint log.
After you restore your site collection, MOSS may need to reset how it points to pages. To correct this issue, you need to run two commands. The first is an stsadm deletecontentdb – this command is misleading because it does not delete your contentdb. Once you run this command, then run the addcontentdb to restore the links.
Here are the commands
Stsadm -o deletecontentdb -url [URL of your site collection] -databasename [Name of Your Content DB]
Stsadm -o addcontentdb -url [URL of your site collection] -databasename [Name of Your Content DB]
After you complete the two steps above, verify all the assemblies referenced in your code are available in the assembly GAC. These two addressed this issue. I hope it will help someone struggling with this weird error message.