Well after working on this thing and not making any headway other than thinking I repaired the water leak, I was frustrated and took it to Nathan at a local shop, East Texas Street machines that does LS Swaps and has more experience with the software side of this than I do.
Nathan found a few issues with the tune and fixed those but also found a misfire issue that has to do with #1 & 5 injectors. I picked it up to swap injectors and figure out the injector circuitry trouble code. Other than that, it runs and shifts fine now.
I have another water leak, looks like a pump gasket on the other side in the new gasket that I just put in...
More to come...