what do I need to do in order to use the GitHub Version of the Engine with my Project that i originally created with the launcher, so i can see the links to header files in BLuePrint nodes etc, like I would when I compile the Engine from Github?
If you start the github compiled engine, it should fin the project itself. Otherwise jsut use file-> open project -> and find the uproject you want to open.
what I did was after compiling the github engine I right clicked the uproject file and selected switch unreal engine version. After that you browse to your github engine folder. You may have to re-generate your VS2013 project files!