What makes using OBD2 system, so much better than OBD1

How/ or where do you get an ECU flashed if you modify cam/injectors..etc ?

You find a company that supports it. Mopars I don't think were over supported. Back then I had a 92 GT mustang and Chips were common. I know Mopar had some performance ECU's.

If your just looking to go to a modern electric controlled trans there are stand alone controllers.