I can try and answer some of your general questions about modules.
Unfortunately adding new modules is currently a very manual process. I wrote a small “how to” for adding a new editor module, and the process for a runtime module (like the one you added) is very similar. What is the proper method for extending the Editor Engine? - C++ - Epic Developer Community Forums
There’s some more information about the source code layout used by UBT here: Explanation of Source Code folder structure? - C++ - Epic Developer Community Forums
The class wizard in the editor is (as of 4.4) able to add code to any module referenced by your .uproject file.
You shouldn’t need to mess with the Visual Studio solution. Providing your module is referenced by your .Target.cs file (see my previous links), you should just need to re-generate your solution and it will be updated as appropriate (you right click on your .uproject file and choose “Generate Visual Studio project files”. If this option isn’t available, then make sure you’ve run UnrealVersionSelector.exe for the UE4 build you made - UE4/Engine/Binaries/Win64).