Hi guys,
I've done a gen 2 to gen3 ecu conversion with a berk jumper harness and code 21 and 31 shows up.
I know 21 is the oxy sensor, my main concern is 31 which is the map sensor.
I have fitted all the gen 3 parts required and they were off the same car in good work condition. 
Car starts and idles fine but at 10.8 afr, won't rev and blows black smoke.
 

I don't know anything about the Berk harness but I would suggest the cold start injector needs to be disabled if that hasn't already been done. Which injectors are you using? Gen3 ECU cold starts on the main injectors which are 540s. There is no cold start injector on the Gen3.

You haven't quite mentioned what was swapped in full.
As Falcon mentioned, did you swap the injectors (If not, you will run into problems running dangerously lean).
Did you swap the engine wiring harness? If not, did you change the Oxygen sensor from the single wire one on the original Gen 2, to the 4 wire that that Gen 3 uses? (If not, this is why your getting the code 21 error).
Not sure why your getting the 31 error. Have you tested the map sensor separately (Are you sure its not a dud)?
 
Whilst your at it, check base timing is set to 10 Degree's.
If you feel in a good mood, retard the exhaust Cam 5-10 Degrees too. (This is an instant 5-10hp on a Gen 2 engine)