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Could the motor just be swapped in or would the electrical "brain" from the E12 have to be installed as well? Any other issues?

Should read CSI

From what I've read you can swap the engine directly just fine. Take a look at the labels on the ECUs, they should be identical as the years are the same. If they're different (either number, color, or both) you can swap them out, but because it's all analog it wouldn't make a noticeable difference just slight upgrades in the circuitry. I have used an L-Jet 633CSi computer in my 528i for testing and it was fine, the wiring is almost the same with the exception of the aux air valve, but that's just jumpered from the fuel pump + and not related to the ECU anyway.

Thanks for the info