Most of your reply is correct, except this first part:
starters it built upon Virgin/Vector Grafix's Shuttle.
SSM has been built from the ground up. AFAIK, the only thing the developers used from Virgin's Shuttle is the inspiration.
All the procedures, panels, checklists, etc... come from official NASA documents, which can be found on the web, or can be requested from NASA itself.
-Toine