Are you seeing the mojoPortal page for 404 errors or are you seeing the IIS default 404 page?
If you created extensionless urls on your dev machine, those would probably result in 404 on Win 2003 because it does not support extensionless urls for ASP.NET without some custom configuration or isapi filter.
Is it possible that you have something else on the server that is redirecting things before it gets to mojoPortal and causing a 404, ie custom url rewrite module or something installed in IIS?
See also Moving an Installation of mojoPortal to a Different Server.
Hope that helps,
Joe