How would you go about diagnosing this problem...

so you’re still using the auto trans ecu? are their differences in the ecu… ie does 1 have a trans controller and the other not, or are they the same.
how does the speedo and tach get its readings from the 2 different trannies?

i am willing to bet that the ecu has a gear based fuel enrichment table.

you may need want to try swapping to an ecu from a car that had a manual