Update, just about finished but having a hell of a time with the fuel pump. The pump is always running when the ignition is ON, it almost sounds like it's idling or something, and when I test the fuel pump output, it gets louder. Same thing when I initially turn the ignition to ON, it'll do the 2 seconds of pumping start Microsquirt tells it to, then it goes back to the idling sound. Wiring all checks out. I can't send an output test to the pump when the relay is pulled. BTW, the way I wired the pump was positive to a fuse, which goes to a standard automotive relay. Negative goes to ground.

I know there was some reverse logic with fuel pumps in standard form, but what does that mean when everything to the pump is rewired from scratch? I'm using zero factory wiring in the fuel system except for the 12v switch ignition to a fuel pump relay.

Any ideas?

check the connections at the relay i would say? also make sure it is a normal relay...many different types that look the same.

control circuit: 85-86: one side to microsquirt wire (which grounds to activate the pump), other side 12V switched. (12V when car is ON)

power circuit: 30-87: one side +12V from battery, other side goes to fuel pump

On my aem, you have a table where you set the duty cycle for the low side (ground) circuit used to trigger the fp relay. The cells in this table are all either 0 or 100. 100 equals full ground to the circuit which in turn activates the relays and fp comes on.
0 opens that circuit and fp is off.

Do you have a table like that in MS to control the fp low side?

i haven't found anything in tunerstudio yet to control that. Don't think it exists.

So it's definitely wired correctly, the relays have been tested and the MS is talking to the pump. After doing a bunch of reading here, it looks like I may just have a loud fuel pump, as I hear it only in the ON position, which is triggering the 12V switch which triggers all the relays, so it's energized. MS does its 2-second priming, and then it settles to a metallic idleness (best way to describe it). It looks like a lot of SCs did this if the air flow sensor switch was bad or disconnected, so maybe it's a byproduct of simplifying the wiring?

Next problem is the car will not shut off when I turn it off. All lights and accessories turn off, but the motor keeps on going. I believe it's the ignition switch, so I'll be digging into that a little more.

Engine has been started tho! Did my first 20-minute initial break-in run. Only had a couple minutes of smoke but cleared up pretty quick and oil pressure seems to be strong. I do have a slight leak somewhere by the left chain housing, which sucks, but otherwise, I'm pretty happy. I need to balance the ITBs and get out and start tuning.