I'm going to leave the transmission alone for now and just drive it like it has to be driven. Once I get some more miles on it (and some quarter mile passes) I'll know more about what is working and what isn't and then I can make a better decision on next steps.

Right now my focus is on tuning the engine. The left side of the engine is running 1 point leaner than the right side. I swapped the O2 sensors from side to side but that didn't make a difference. So the issue is the engine not the sensors. I think one cylinder on the left side has a bad plug or a bad plug wire so I'm going to change plugs and inspect the wires and then go from there. I could also have a weak injector on the left side but I think it is ignition related not fuel.