As for my setup.....
This isn't a guide. This is what I've done. Don't mimic it if you don't understand at least 1/2 way what you're doing.
I finished unwrapping the harness today and started to cut... I build my harnesses for MS from relatively scratch. It's unnecessary but I believe it to be a smarter move. Wanna know why? Well.. .that's another topic in itself. IMHO if you want stand alone... don't go plug and play.
When you start to strip the harness down the goal is to keep the basics in tact:
Starter, charging, connectors to body (which includes starting/charging/gauge sensors)... so what what also left in there was the CSI setup (it's already wired through the STA wiring), coolant temp gauge sensor connector, oil pressure gauge sensor, and the radiator fan switch (which is REALLY odd wiring that Toyota did).
So what do you need for MS:
02, injectors, TPS, coolant temp sensor, air intake temp sensor, ignition
What can be removed from the harness and discarded:
TPS sensor (if using a 4age head then you will need a 4age tps and connector... my 3 wire 4afe tps connector was cut out), 02 sensor (4afe uses a 2 wire and MS uses a 1 wire... I will buy a new o2), diag port, map harness, ignition wiring (all... dizzy/ignitor).
Be wary when you cut the diag port.... in the ae92, oddly enough, they run through the body harness. The fuel pump wire you need for MS is the blue wire incorporated here.... there's a ground and 3 more wires (IG-... which I'm going to guess is the tach, te1 and 1 more.... I didn't mark these other 2 other than 'diag port' for now... I'm guessing they won't be necessary at all).
Cut all of the connectors you need for MS (in my case it's just injectors, coolant temp sensor connector and air temp sensor connector..... be careful to verify that you're cutting the correct coolant temp sensor out as one is directly tied to the STA/CSI circuit... leave that in place).
Car in question:
Engine (note adj cam gears and the 2 piece oil pan... this is an 11.3:1 "smallport" 7age):
harness after unwrapping:
removed and can be discarded:
what is left of the harness and the pigtails:
getting the harness out of the car and to this point is about 3 hours... only because the ae92 appears to be a PITA.... much more difficult than an AW11.