Well I figured it out finally, the company I bought the harness from screwed up and put the wires in wrong in the main trans connector. Luckily I had a factory harness to compare to. The wires were put in 180 degrees backwards in the connector. I had to removed them all, turn the connector 180 and reinstall them. Everything seems to work fine now. I haven't gotten into 3rd or 4th gear yet but it seems to be shifting perfectly fine. Now all I have to do is figure this misfire out....
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Brian Miller
-1972 Nova
-1968 Camaro
-1967 C-10 step side 4x4
-2000 Dodge Dakota
it'll buff out........ 
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