I'm almost willing to bet you have a bad EEC, simply for the fact that you can't get a scanner to connect.
When we did my wife's auto to manual tranny swap a few weeks ago, the EEC we got to go with it was used, and when we tried to reprogram her PATS key (96+ anti-theft key) at the dealership where I work, the Ford scanner wouldn't connect. I bought a new EEC and it connected and everything works fine now.
Granted, hers is an EEC-V unit, but the same theory applies. If it can't connect to the diagnostics unit, most likely there is something fried in the EEC.
Check with NAPA and/or Carquest, they tend to have better pricing and availability on EEC-IV units.
