Had some time to put some stuff on the car.
Also went over the "swap harness" in the engine bay, originally I had planned to wire it correctly, but when I had problems getting it to start I reverted back to the "common" way. I have corrected it today, now the ECU controls/ is controlled by the EFI fuse and relay. There are a couple of other kinks in my engine as of now, so its hard to tell if it effected anything negatively/positively, but time will sure tell.
This is what I had before, made it run but wasn't "correct".
Plugs from bottom to top right (two are from a SC300, and only one wire had a different color):
1UZ Black - EB1, 1UZ Black - EB2, MA70 Yellow - C-1.
Connections from bottom to top:
1UZ EB-1 - Black-Orange and Black-Yellow (runs between ECU and the EFI relay) connects to MA70 C-1 - White (the white wire supplies power to the HAZ Horn),
1UZ EB-2 - White (SC300) or Black Orange (SC400, supplies power to Ignition system) connects to MA70 C-1 Black-Yellow and Black-Orange
1UZ EB-2 - Black-Red connects to MA70 C-1 Black-Red (supplies power to ECU and many other components)
I don't have any good pics of the "corrected" wiring, mainly because I soldered two incorrect wires together, haha. After fixing that I then continued to wrap the harness up and the camera slipped my mind, but here is the "correction":
1UZ EB-1 - Black-Yellow and 1UZ EB-2 Black-Orange(White) connects to MA70 C-1 - Black-Yellow
1UZ EB-1 - Black-Orange connects to MA70 C-1 - Black-Orange
1UZ EB-2 - Black-Red connects to MA70 C-1 - Black-Red (remained untouched)
Aside from the odd Black-Orange(white) wire, it was simply matching colors.
Here is a shot of the harness loomed up again:
