Sounds like you downloaded the mojoPortal package for .NET 3.5
If you download the package for .NET 4 it should not prompt to upgrade to .NET 4
The 9th and 10th items in our FAQ also have some information about this problem.
Though as Aaron said for real development its best to work with the actual source code in Visual Studio, not with the pre-compiled packages. See also our article Understanding the Differences Between Deployment File and Source Code
Hope that helps,
Joe