Ford Repair: 1991 Ford Explorer EEC Relay, red hot wire, blown fuses

Question
Stopped to get fuel the other day and it wouldn't start. Noticed fuel pump not humming as I can hear mine inside my truck. Got it towed home and after further looking the ECC Relay was blowing. Traced my wires to the harness that goes to the transmission (pigtail connector located on drivers side wheel-well). The Red (Hot) wire was melted inside the connector. Fixed that and still had blown fuses. so I unhooked the harness from the tranmission and the 3 prong rectangle plug was shorting out not the round connector. Bare wires exposed. Red wire in the center of the plug has melted. My question is what does that go to and how to check to see if it still good. I've rechecked the circuit and no fuses are blown, but my fuel pump still does not come on.
Fuel pump was replaced during this process and Tranmission was rebuilt 6 weeks ago and that how I think the wires got exposed.. Thanks you

Answer
John,

I am not exactly sure which three wire connector you are refering too. Where is it located on the transmission case? I am thinking when they rebuilt your transmission that maybe one of the solenoids got pinched to ground or has shorted out.

Have you tried jumping the fuel pump relay just to know that circuit is good?  

Let me know what you find.