UPDATE
I have been running the Samurai for several months now with its current setup:
1.6L 8 valve with the sidekick intake manifold, throttle body, and associated sensors. I'm running the Samurai distributor, coil, and ignitor (the ignitor is different on the sidekick, and won't plug into the Samurai's harness). The IAC valve is capped off (the Samurai ECU keeps it open too much, resulting in a lean and unstable idle). The TBI butterfly valve is opened up a little bit for a good idle. I'm running the stock 1992 Samurai ECU and wiring harness.
My Samurai is quite a bit heavier than the average one (exo cage, winch, and other armor). I've had the Samurai on all sorts of terrain, from Sea level here at the coast to over 14,000ft. in Colorado, with a bunch of off road and street miles logged. It runs great...more low end torque, more high end HP, added about 20 MPH to my top speed (about 80 MPH on flat ground) and it will hold 55 MPH on a 5% grade (drops a bit on steeper grades). It gets about 15% better fuel economy than the 1.3L did that I pulled out.
I have no complaints with this setup, but I feel that slightly better economy and maybe a few extra HP are possible with a proper functioning IAC valve and proper fuel mapping with the sidekick ECU. So, in the interest of testing, I pulled up the pinouts for both the sidekick and Samurai ECU's and went to work. (see attached documents)
After comparing both schematics for about 20 minutes, I determined that there were 7 differences between the 2 wiring harnesses. All of the important things were the same (power supplies, MAP, TPS, CTS, etc.). The sidekick had the fast idle power steering input and EVAP system controls that the Samurai doesn't, and a few other things. But, I thought there was a chance it might work without modification.
The connectors between the two ECU's are interchangeable, so the sidekick ECU plugs right into the Samurai wiring harness. I plugged it in and turned it over; it would fire and then immediately die. If I continued cranking, it would crank for about 1 second, hit on about 4 cylinders, then go back to cranking, then hit on 4 cylinders, etc. I plugged the ECU fuse in and got code 12 (meaning the ECU was powered up and operating, and had no trouble codes). After doing a bit of troubleshooting, I discovered that after a few seconds of cranking, code 41 (weak or no spark) came up consistently. I spent some more time looking, and realized that the tach signal on the Samurai harness went directly to the instrument cluster...but in the sidekick it went to pin A1 on the ECU. Pin A1 on the Samurai harness was unused. So, I pulled one of the connectors out of the sidekick harness, inserted it into the Samurai's A1 spot, and ran a jumper from the tach signal wire to the connector. Bingo! It fired right up and ran perfectly, no trouble codes.
I intend to run the Samurai this way (with the sidekick ECU) for the next week or so and see if I notice any driveability/economy issues. I'll be sure to report back here with my findings!