OBD2A auto vs manual ECU

[markodude]

HI all
I am referring to P2E-G01 and P2E-G51 Civic ECUs from 1996 D16Y7 Civic Coupe.
Does anyone know what exactly is the difference between the auto and manual ecus? Are the maps different? Does the auto change maps depending on which gear it thinks you are in? Why would a manual ECU not work, but an auto is fine (the car is manual now)

Background
Did a swap auto>manual y7, took engine with all ancillaries/gearbox/ecu/engine side harness from working car. Put in my car, car wont start with manual ECU. Car starts and runs with Auto ECU but is running extremely rich and blows black smoke at high rpms (comp/leakdown tests done, new HG and valve stem oil seals fitted, MAP sensor replaced).
I have the "auto trans lockup" CEL as expected, but other than that I dont know why the car is running so badly?