Another thing to look at is set the TCM 461 Pattern Type B back to stock (which might be cruise? You'd need to check that). This could well be your issue, I know from what digging I've done if the pattern types are changed you push the shift table look up pointer to a table addresses that is either not mapped or is one of the obscure shift types like safety shift etc.
Failing the above and my post before this one; what happens if you use the same hardware in the good vehicle and with the last tune you posted 'As Is' and write entire both ecm and tcm on the vehicle with the fault?
Some of the stuff that has me confused as to why it would need changing if these swaps are the same...
