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The reason why you get a 404 page not found after upgrading from asp.net 3.5 to asp.net 4.0 running on IIS 6.

...and one other issue you might experience is: Server Application Unavailable

IIS 6 and ASP.NET framework 4.0: a few things to take care of

• Install framework asp.net 4.0 and restart
• IIS 6.0 console should now display ASP.NET 4.0 under tab "ASP.NET"
• Under Web Services Extensions (in IIS console) .NET 4.0 framework might be set as: prohibited. This must be ALLOWED otherwise a browser might just return the error 404 page not found which is not very descriptive
• ASP.NET 4.0 applications must be run in a separate process (Application Pool) otherwise you'll get the error 'Server Application Unavailable'. The Windows event viewer will list such event, see screenshot below

Best regards
Cheers, Frank