Your '86 TRX CDI should not plug into your '85 ATC harness. So I am guessing you are running your ATC CDI?? Are you running the coil from your TRX as well or are you running the ATC CDI?
What you are describing sure sounds like a fuel mixture issue to me, whether it be a jetting issue you need to dial in or as suggested, you may have an air leak somewhere that you haven't found yet.
You shouldn't have any issues plugging on your 86 TRX engine harness to your '85 ATC chassis harness, or running your '85 coil. If your '85 engine ran fine too, then I would say electrical is probably not your problem.
The ATC pipes are different than the TRX pipes and may require different jetting specs to dial in right. But having said that, I would expect the differences to somewhat small.


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