Another good way to test if its something to do with the injector (I know you replaced the injector so its not that actual part) is to pull BOTH injectors out at the same time but leave them plugged in.  Get a couple of empty water bottles or something like it and stick 1 injector in each bottle (you may need to secure them to the bottle with tape).  Now crank the engine over for 20-30 seconds.  The 2 bottles should have the same amount of fuel in them (or within 1 spray of each other)  If it is VASTLY different you will be able to tell right away.  From there its either got to be the ECU or bad wiring i would guess. 

I agree with (chuddley).
Is it throwing any weird or improper codes? Like a faulty temp. sensor?
When I had problems with my Massimo running fat, I replaced the injectors and it still ran rich-wet plugs, glowing exhaust.
After I got out the ohmmeter and started checking everything by hand. I realized that the stock ECU was not capable of pulling itself down enough to lean itself out.
First off, verify that the CORRECT injector was properly replaced(matching numbers).They need to be same same or will run rich.
Since the vehicle has been torn apart how many times, I d look at the wiring, check for continuity from part to pin on the ECU.
Verify with a volt meter that the O2 sensor is working.
If the wiring all checks out ,you may have an internal ground issue with the ECU.

ECU was already swapped. So was the injector and the o2 sensor. Even the MAF and crank positioning sensor just to be safe.

I haven't had a chance to get back at it but I will try all these suggestions

And yes NM. We out this one back to stock.

when we pull the plug boot there's ZERO change in the way the engine runs.

So you have not swapped or replaced coil to confirm proper operation??

Sounds like coil to me.

UPDATE:

Swapped the flywheel because the wrong one was in the engine. The EPS flywheel has a narrower magnet, which was causing my NON-EPS stator to not charge the battery. Still, no change.

Swapped the coil, made no difference. Put on a new throttle body with new auto-enrichener and TPS, still no difference. Checked compression again, both cylinders still at 150+lbs of compression (according to our gauge).

We swapped the o2 sensor again, thinking the gas contamination ruined the other new one, and no change. Swapped the crankshaft sensor, and again, no change.Gone through about a box os spark plugs now as these things keep getting wet fowled.

Have you put a noid light on the injector connector yet?