My 2007 E is running on 2 cylinders, help!

As the title states, my E (2007 150k miles, Fwd, 3rd owner) is running on 2 cylinders, number 2 and 3. It starts and runs but has poor acceleration, the mpg has been cut down from 22 to 13, trouble getting into gear 4 and 5 (speeds exceeding 60 mph), and idles rough.

I had a P0301 show up intially and later pulled a P0171.

What I have done so far: Swapped around coil packs and plugs. No change. Replaced plugs and did valve adjustment. No change. Did wet and dry compression test. Results good, in spec. Swapped injector 1 to 4. Power loss occurred here. CEL disappeared. Replaced O-rings on injectors, ran through injector cleaner. No change. Reattached a bracket that fell off at some point with throttle body wires connected to it. Idle improved and intermittent stalling stopped when shifting from park. Cleaned IAC and throttle body. No change. Tested fuel pressure. Results good, in spec. Did fog test for vacuum leaks. No leaks. Did noid test. Failed on injector connection 1 and 4. Continuity good on new injectors. Old injectors seemed to work based on test but replaced anyway. Had E running and unplugged injector 1. No change. Repeated for injector 2 and 3, stumbled and died. Repeated for injector 4. No change. Tried 1 and 4 at the same time. No change. Tested voltage for each injector. 12v for each. Cleaned the grounds coming off the battery. No change. Disconnected battery for 10 minutes. No change. Live data stated fuel pump relay was off while idling. The fuel pump relay main turned on and off with car.

Not sure what to do next. I am thinking ECU but cannot find much information on two injectors not running while car can start and drive. It still is chugging gas, running rough but not as rough as before doing things, and has poor power output. I've been working on it since January and it seemed to have happened overnight with VSA light and CEL coming on intermittently but never staying on. Did have some days when it wouldn't start up right but would start up fine after shutting it off and then back on. But I didn't drive much November or December so I figured it was the battery.

So I am at a loss as most ECU issues seem to be a no-start or misfire codes. My car is currently not throwing any CEL and hasn't thrown CEL since swapping the injectors the first time. I have read the P0171 but it gave no CEL. It also detects misfires on live data but no codes otherwise.

Any help would be appreciated.