Okay, now that I have a frame of reference, I see what you're talking about in post #5. You're right, there aren't that many things to swap out. There's as much reconnecting as there is discarding of pins.
I think the next step is to verify that those pins are in fact the only things that need to be switched (i.e., different hardware at the ends of the terminals). bmw_chuzo has a thread documenting his M52TUB28 to M54B30 swap. During the swap he also changed over to the MS43, but its unclear whether or not he reused the sensor from the M52TUB28 block. When I was browsing his thread documenting the swap, he mentioned that the older style alternators have a 3 pin connector and the newer style have a 2 pin. Otherwise, it looks like the swap involves only three things: Instrument cluster reflash, EWS module, and DME (EWS and DME must be paired).
Does anyone know what else we need?