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Like normal.
I still use the little blue connector under my dash.
thats what I have, and what I use to jump my system to check codes, but I don't know anything about timing the motor by it...
Contact RyWire and ask them. It's possible that your timing belt's off a tooth or two.
Hmm. I don't know what to tell you, dude. I don't have to flip my CEL toggle switch to set my timing (JKOBD/RyWire OBDI harness, '91 hatch). I use a 3" piece of scrap engine harness wire with about 3/8-1/2" stripped off each end to jump my timing connector. Works the same as it does on my woman's stock '90 hatch.