Not sure if i totally understand what you are asking,
but you will need a new ECU and subsequently a new EWS that will be able to be paired with the new ECU that is for the MS43.
You may be able to run a used MS43 ECU and MATCHING EWS, and then recode all the modules on the car to reflect the new index coding
bmw chuzo on the forums put a 330 motor in his 325 and went through the whole deal with electronics, you may want to search for his thread and hit him up for some tips
best of luck