Every time you disconnect the battery or reflash the ECM, the trans has to relearn.
Make sure the fuel filter is good, and drive it. It should get better.
Probably a broken/shorted wire from the trans to the TCM. follow the harness and inspect for damage. Pull the inner fender for better inspection-- if the harmess is OK at the trans.
I like the extra fluid in the deep pan. Does it run cooler-- maybe not, but it doen't hurt either. Some say it takes longer to cool down, so what difference does that make? Allison made it for a reason. :hug: