The original flex plate won't work because it's not balanced properly for the post-1982 engine. (It's 28oz instead of 50oz like the Explorer engine).
You can either have a machine shop rebalance it or you can get ahold of Art Carr at 800-278-2277 and ask for P/N23115 Mustang II 141 tooth 50oz. imbalance Flex Plates for putting a 5.0L H.O into a Mustang II with a C4.
If you do one of those two things, the engine will bolt up (also use the '96 Explorer harmonic balancer, not your stock one).
you would be better off running an 87-93 mustang computer and harness. I don't know enough about the Explorer computer to make a good recommendation on how to handle the vss.