I just did a clean install myself after reading the thread about not installing in the 86 programs folder. I installed off a disc tho not from Steam.
The only thing I can think of on JSGME is to make sure you install JSGME into the SH4 master folder and activate it from there. If you activate it from a screen short cut, it will look like it's putting it in, but it's not.
Also with TMO you need the TMO Small patch which fixes a command progression bug. Without it, if you have a TAMBOR Class boat and get offered a new command it actually regresses you back to a SALMON rather than ahead to a GATO or BALAO. Here's the link for that:
http://www.subsim.com/radioroom/down...o=file&id=3506
Good luck.