Electrical Nightmare

Well I posted yesterday that I thought I had a Fuel Pump Relay situation, we read up on some stuff and called a shop that was willing to help with my 1998 Eclipse GS- he suggested hooking up an OBD2 System Scanner and seeing if there are any codes, we hooked it up, a fan started spinning and "POP" smoke flying everywhere. The smell, gross. The ECU was smoking. Electrical Problem? That is what I am hearing. I am gettin a deal on a new ECU, that is the good news, the bad news is no idea where this electrical situation is starting, been over every wire 6 times and seems ok. Would a new wiring harness be safest move? I need help. I need to get this car running, it has been sitting for 6-months- all this just for changing the Head Gasket. Any advice would be appreciated. Let me know if anyone else has ever experienced this because the guy I am talking with says he has never heard of anything like this before!

Thanks
Kel

If there was smoke coming from your ecu then I would definatly start there. A new wiring harness may not be neccessary but it may be the easiest(quickest, not easiest) way to diagnose the problem. You said that you have gone over the wires, so there are no grounding problems or cracked insulation. Never seen an ECU start smoking but I have seen a Dist. cap catch on fire shortly after "the dealer" put a new one on my step-dads truck. weird!?! Let us know how it goes.