You should be able to do a stand-alone swap of a Gen 2 transmission with its ECM. The wiring going to and from the ECM isn't as complicated as it would seem.

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One issue is the mechanical/electrical speedometer interface. An option that I can think of, BUT HAVE NOT VERIFIED, is to use something like an Autometer speedometer sender. It's made to give a pulse output from a transmission that had a mechanical cable output, but still has an output side that you could hook the mechanical speedometer cable up to. It may require some custom speedometer cables to be made, and I don't know if it gives the correct pulse output.

I'm leaving the Gen 1 transmission in my truck for now, and just leaving the Gen 2 transmission wiring disconnected until I'm ready to do that swap. Though, I plan to swap the electronic speedometer sender and the gear indicator switch over in the meantime.

1989 Mitsubishi Montero SWB 0.0L (3.5L soon?) Auto, Front LSD, Rear SR Locker, Aisin hubs, Safari Snorkel, ARB Front Bumper, Warn M8000, Bushwacker Flares
1984 Mitsubishi Montero
2005 Dodge SRT-4
1970 Plymouth 'Cuda (in pieces)
...and a few others less interesting.