If you want to work with the net40 solution you have to replace the contents of Web.config with the contents of Web.net40.config before you can build the solution, and you may have to do the same in other projects like mojoPortal.Features.UI and WebStore.UI, which also have Web.config files.
Note that .NET version is confusing because even .NET 4.5 is identified by version 4, ie if you install .NET 4.5 on the server it will still show up in Administration > System Info as version 4