Ran into this today and it’d been so long since I’d fought with this issue, it took me some time to re-figure it out.  So, as a reminder to myself…

If you’re getting a 404 Not Found on an ASP.NET application running on Windows Server 2003/IIS6 that should be working just fine - the files are definitely there and the permissions are correct and everything - don’t forget to make sure ASP.NET is enabled in the IIS Administration Console under “Web Service Extensions.”

If you uninstall and re-install ASP.NET, these settings get reset to “Prohibited” so ASP.NET won’t work.  You’ll need to change them to “Allowed.”