When you clone the repository, there are only 2 branches, the default branch which you should use and the joedev branch where I work. Whenever my branch has new stable changes they get merged to the default branch, the default branch is meant to be stable and up to date.
Once you have the code, you should review the READMEVisualStudio.txt file. It tells how to use 3.5 .NET, basically you need to use the mojoportal.net35.sln which will compile it for 3.5, but, you also need to replace the contents of the Web.config file (which is pre-configured for .NET 4) with the contents of the Web.net35.config
This is explained in the readme file and also in this blog post
Hope it helps,