firejackal

I'm currently stuck on an problem on my 2JZ swap.
I can't figure if it's my wiring, or the ECU itself.

TLDR: Having issues with ECU; +B/+B1/IGSW, with +B/+B1 wired properly car won't shut off after key is taken out. IGSW doesn't seem to do anything.

Some basic information first and to prevent further questions:
* Everything is out of a 93 SC300
* I've used this engine/ecu before in a different car (mk3 supra.)
* I did the wiring myself because it's straight forward and I've done it before plenty of times and can solder perfectly.
* Ran the car for years on it's stock KA motor.
* Wiring to the ECU is the same how I had it before, I double checked the pinout to made sure of this and double checked this with the pin numbers on the back of the plugs.
* Can't afford a stand-alone or piggyback ecu at this moment.
* Double checked the IAC wiring, etc.

And the current wiring specifics:
* Instead of using the F3 plug's ignition output for sensors, etc. I'm maintaining the use of the M-REL function of the 2JZ ECU, I have a extra relay wired in where the ECCS relay would of been (since that was part of the S14's stock harness) and so I will call that the EFI relay.
EFI coil input directly to ECU's M-REL with nothing in between.
EFI coil output directly to ground.
EFI switch input directly to the battery (I need to add a fuse later.)
EFI switch output to the engine sensors.

And now the issue:
So I was having starting and idle issues and noticed the 2JZ ecu is suppose to keep power to the M-REL for a few seconds to fully open the IAC valve.
That's when I noticed I had the ECU's +B +B1 on the car's ignition signal instead of the EFI relay switch out.
So I did that change, idles/starts better but now the engine wouldn't shut off when the key is taken out.

So I was doing some testing...
1) Recap: +B +B1 to ignition allowed everything to shut off, but ecu wouldn't keep power to M-REL afterwards.
2) Recap: +B +B1 to EFI relay switch out didn't allow car to shut off.
3) With car running, I "disconnected" the IGSW wire to the ECU, and the ECU didn't turn off, still outputting the M-REL voltage...... Which makes it seem like to me the IGSW signal on the ECU was not operating correctly. Which is why I thought maybe a bad ECU now or a shorted signal in there. But I opened it up, and found no evidence of bad traces, leaks/etc. Board was still covered in that protective layer.

I even tried switching the signal for the fuel pump to ignition (I have it on it's own relay for a better 12v source) and the car stays alive for 5-8 seconds after the key goes off.
(The 2JZ diagram has the fuel pump off the EFI relay.)

So, does anyone have any ideas why this is happening, or maybe came across it?
I checked for things like a voltage feeding back, and didn't have any feed back with the car's ignition off.
I'm out completely of ideas.

Thanks in advance