Is that the AEM EMS (universal) or one of the plug and play modules? I think a new SC400 harness is going to cost you way more money than its worth in *possible* time saving. I think I remember a new SC400 engine harness being around $400 or so, but I'm just guessing at what I saw once...
With some tape, a sharpie and a 100ft roll of wire you should be able to complete the entire project in a weekend...
Once you have the milspec harness all hooked up and boxed together on the engine (including keeping notes on the pinouts), all you should need to do is get a short pigtail for the ECU (12 inches would easily do, with each wire labeled) and splice the wires to the correct "pin-ins" on the ECU and it'll be good to go, sensor wise. Then you're going to need to set up relays for the associated electronics (ECU, fuel pump, etc).
I'd suggest only minimal "interfacing" between the Supra's
already-installed harness and the engine management. You'll need signals for the basic things like the ignition, tachometer, battery voltage, oil pressure and water temperature, but those shouldn't be too difficult to figure out after you have the engine completely hooked up (not sure if your ECU has in/outputs for this).
Since I don't really know where you're at with the project (and my advice could be called sketchy at best) I can't really help but muddy it up. I've been planning how to attack my 1UZ->4Runner harness for a while and I plan on setting up the engine to be 98% standalone from the truck with only the ignition and relays changing slightly. My primary concern is not messing up what I've already got working for me. This means I need/want to set up a relay for the Ignition and have it feed all my supplementary relays (Including the chassis wiring, ignition, computer etc).
Regardless, I'm sure you have it planned out much better than I do (in my head) even at this point. Don't go too hard on me, its been a long day

...