I was thinking the same thing about leaving the tunes on for the sake of a happy shift pattern, but I am concerned about the thunk when going into R or D. I did find this information that seems pretty reasonable.

TorqShift Transmission - Information and Troubleshooting - Ford Truck Enthusiasts Forums

I think it's worth a look. There were two things in there that really applied to mine, hopefully they are what's at issue here.