Okay.
There really isn't that much in the way of extraneous emissions on a Renix other than the EGR and the cat. There are no electronic evap valves, purge solenoids, secondary O2 sensors, etc like you find on newer vehicles. If you're staying with the Renix FI, then you need to keep all the sensors. You can go through the harness and strip out all the wires for accessories that you remove, but that seems like a lot of work. You can trace all the wires on the yellow diagnostic connectors under the hood back and cut them.
If I were to try to transplant the engine and FI system into another vehicle, I'd probably keep the engine bay harness relatively intact. For the section of the harness inside, I'd either eliminate the C101 connector, or just chop the harness just inside and splice just the wires I need for the PCM. Or maybe just mount the PCM in the engine bay in a watertight container. I've seen a few folks use tupperware and silicon.
Other things you could delete. Get rid of the temp switch on the fan and either wire it always on or have a switch in the cab. Rip out all the vacumn lines for the hvac stuff and eliminate the vacumn ball and the evap/charcol canister. I'd keep the vacumn lines from the valve cover to cut down on blow-by, the line to the map, line to the fuel reg, and the brake booster and cap any the other lines off.
The trans computer is pretty much standalone, other than getting an input from the TPS sensor. You could go with an AWshifting setup and eliminate it altogether though.
How are you with wiring and reading a wiring schematic or tracing wires? I don't mean this as an insult, but there are many folks who go numb when thye look at a wiring schematic and don't know what a voltmeter is. I think some skill and understanding of how the system works is a must. Otherwise I foresee you coming back in a few weeks with a posting titles "I simplified my wiring harness, now it won't start".