'99 Mach Z Electrical Issues

So I have recently aquired a '99 Mach Z that won't run worth a hoot. Backfires, spits, will not rev up to engage the clutches. Now I've chased this electrical issue all around and started with the DESS, I have now replaced every part of the electrical system except for the wiring harness.
I had it running backwards for a short time, until I adjusted the gap, then it started running forward, but still spitting and coughing.
I had a spare trigger coil and bolted it into the bottom location as the stock one was on the top location. With both installed and the new one plugged in, the machine ran, idles perfect, even spun the track. Thought I had it figured. However, after removing the stock coil(with the new one on the bottom location still)the machine would want to run backwards again, so I changed positions(to the top) and started it back up.......runs like shat again. Won't engage etc. But running forward.

Now before this I had tried a new coil but it didn't make a difference at the time so I continued swapping old electrical for new, brainbox, coils, stator, everything. Like I mentioned, only thing left is a wiring harness. Has anyone experience with these sleds? I really want to start building my drag sled but won't transplant the motor until I know it's sound and running proper.

Any help is appreciated.

Took a different flywheel in the end. Thought the crank was out of phase. It was a mis-timed flywheel. Apparently the one I bought was for a RER sled. This is not. Once we figured that out she purrs like a kitten. Thanx to Robbie and my old man for working on the thing all day before finally figuring it out.