I guess this is not a production server. Otherwise, I cannot imagine you have done so much on it.
First, .NET 1.1 is still supported on Server 2008, but please carefully follow our guide here so as to configure it correctly.
http://learn.iis.net/page.aspx/472/how-to-install-aspnet-11-with-iis7-on-vista-and-windows-2008/
Second, I am not sure if your web sites are bitness sensitive. If you run that under 64-bit mode and do experience some server errors, it is highly recommended to create a 32-bit application pool and assign your web sites to it so that MOSS and your sites can run separately.
Hope this help.