I've been working on a gen 4 lc9 ls swap into my 93 jeep, and while all Is going smooth with the majority of it, I've got a bad feeling with my transmission. As the title suggests I am running a 6l80E with the motor, both are out of the same truck, and are the original for the truck. I first did a bench harness setup to read the ecm into my laptop, and at first I was just doing the vats delete, so I hadn't even thought about not having the tcm plugged up with the harness. I have since written to the e38 ecm with the complete harness hooked up to the motor/transmission/battery. From everything I've been able to find, and my truck not having a separate tcm, this meant the tcm was made into the trans or part of the ecm. I tried again to read the vehicle because I wanted to look into getting the manual shifting switch enabled for crawling through trails when it's all said and done, but nothing comes up for my transmission other than the two basic options of General and Manual(I'm not 100% sure this is the other option, I'll load the tune on my pc when I get back to it.) I downloaded a 2013 Chevy Silverado 1500 5.3 auto tune from the repository and it has the trans tune with it. I saw that and felt disheartened at the thought of not having the trans working when I get it in the yj. Im brand new to tuning and more of a ford guy myself so im not real familiar with how the ls stuff works but does this seem like there's an issue with the transmission? My initial thought was I overwrote what the tcm had with 0s since since was no data in the tune I wrote to it for a transmission.