It is over 2 years since you posted the "?" reading for cylinders 3 and 4 and a "0" for 1 and 2. If you see this message, did you get it solved? I now have this same reading for my MGTF 160 year 2002 and only 74000 kilometres on the clock.
I have done some investigation, and I think I know what the problem is. The next release of pscan will use a different way of calculating misfire count. Until then I think that it's probably best to not use this feature.
from memory I think you can code upto four, so either faulty or not compatible. There are different part numbers, like 3TXA, 3TXB, 3TXC, 17TN and not all fobs are compatible with all cars. Also there's 315 and 433 MHz.
Reconnect the old 5AS
Log into the old 5AS using pscan.
Use the "read EMS" feature in pscan and note the EMS.
Fit the replacement 5AS.
Log into the replacement using pscan.
Use the "write EMS" feature in pscan to set it to the value from the original one.
Once you have done this the engine ECU should recognise the replacement 5AS because it's sending the EMS code that the engine ECU expects.
You might have to turn off the ignition and lock the car for the new one to load.
If you already have a pscan then defintely, yes. An OBD socket is under £5 on ebay or Amazon.
It's much easier to calibrate the MGF EPAS if you have a pscan. There's a video here
Just try to make sure that the OBD socket (and therefore pscan) is earthed as near as possible to the earth of the ECUs that you are using. This can be a problem with MGFs because the engine ECU seems to be earthed a long way from the socket and it causes problems. It isn't such a problem with front wheel driver Rovers for some reason. pscan doesn't really care about chassis ground, it's trying to talk to ECUs so it's the ground of the ECU that counts.