Chris,

I can tell you for a fact that it's your wiring harness issues.

I've installed numerous MAF or Fuel map altering computers for other SuperCharged and TurboCharged cars, and EVERY SINGLE ONE INSISTS on the use of solder for the connections.

The reason is that the signal that comes from your MAF or Karman Sensor is a waveform, NOT a pure on/off voltage signal. If the contact is not PERFECT, the MAF reading will be off horrendously, and this causes VERY poor fuel metering. A couple of the installs I did were done like you said, 'wrapped and taped' and brought to me problematic. Proper soldering and shrink wrap session fixed it all.

This is where your wierd idle comes from. (seen it before; change in metering happens to fast compared to throttle response, and you stall)
This is where your misfires are coming from. (seen it before; overly rich metering)
This is where your flashing CEL comes from. (seen it before; too lean and you're knocking bad)

Coupled with a Supercharger or Turbocharger, you are thus led directly into the realm of short or overzealous fuel supply and HEAVY pre-detonation (knock) from erratic fuel supply at times (as shown by wierd exhaust patterns for burnt fuel levels)

These are all bad things that can lead to VERY bad things in a forced induction motor. Your highest immediate priority is to resolve this.

If you don't have a soldering iron, and the experience, let me know, and I'll do it for you when I meet up with eventually; a good ECU soldering job for 30 to 50 wires should take NO LESS THAN AN HOUR when done right. I know this sounds like alot of time to invest, but each and every connection should be treated with that much care; the ECU's job is that important when making sure it can 'hear' or 'talk' to every connected component properly.

E.