If you have both .NET 3.5 and 4.0 installed on the server, then the way to configure the site for 4.0 is to change the application pool to the ASP.NET 4.0 application pool.
Upgrade to the latest mojoPortal while still running .NET 3.5
Then install the latest mojoportal NET 4.0 files on top of the existing installation.
Then change your application pool to a 4.0 application pool.
Of course backup everything first in case something goes wrong so it is possible to go back.
Hope it helps,