I installed a wranglerfix in mine and also had issues with the shifting. I started pulling the harness out of curiosity and found wires had been pinned in the past and they had been left to the open air and moisture. I pulled the whole harness out, laid it out on the garage floor and spent a few days going into detail and repairing the whole harness.
After that I still had a shifting issues and pulled the transmission and replaced the internal shift solenoids. Naturally since it was apart I got a hold of Sonex and ordered every goodie I could find and some new clutches and it's been a rock star ever since.
Until last week it started acting funny, tossed random codes and started getting jumpy. Ended up being a bad battery. Replaced that and all is good again.
Good luck with yours.