I've heard others complain as well. It doesn't shift ideally, but you might try just reconnecting the stock harness without a programmer. My truck shifts alright without a Baummanator, PCS, Suncoast or any other expensive transmission controller. Simply left it alone. It shifts primarily via the VSS.
I'll probably add a manual switch to lock the converter, though it is locking now. Feels like it is in 3rd gear by 20 mph due to the converter locking and unlocking, shifting sort of firm.
After visiting at BTS, i learned to shift manually most of the time anyway. I may have my computer or a chip reflashed after i have settled on some more mods with the engine. Anyway, you might just try going back to stock and see what it does. Hasn't been bothersome yet in my truck, no bogging.