LS1 performance issues in Jeep

[Mitchell1983]

Hi everyone, I'm new to the site and new to LS1's. I have a 1988 Jeep Wrangler with a factory 2000 Trans Am LS1 and 4L60E in it. It was a monster when I bought it, but I kept having problems with the speed sensor, and the wiring going to the transmission. When these issues happened it was permanently stuck in 1st gear. I figure the easy permanent fix is I put a Transgo HD3 full manual valve body in it as it had such great reviews with a B&M megashifter since I thought that would be fun slamming gears anyways and they look cool. Well, now my brakes are incredibly weak and the power is absolutely terrible. I called up Transgo and they mentioned my computer is going into reduced power/safe mode due to not seeing the transmission anymore. This is also causing a loss of vacuum which is why the brakes suck. So, I buy a custom tuned computer with a manual transmission base line, no smog pump, no AC, Cat delete, and rear O2 sensor delete. The engine runs much smoother, brakes are still pretty bad and the power still sucks. I'm out of ideas other than returning the computer to the stock one, getting a new wiring harness, and taking the manual valve body out. I was hoping not to spend that much as I already have too much invested. Do any of you have any opinions or advice? Thanks!

[Cutlass]

thats a weird problem. I'd probablly just put it back to stock