01 ford ranger 2.5 4cyl. high idle lean condition

I have an 01 Ford Ranger 4cyl. 2.5 that wouldn't run the evap monitor and had a p0171 along with p1506 and a bunch of body codes that didn't make sense. I repaired the vacuum leaks I found but the screw in the throttle body had been messed with so I went on to set the minimum idle because the iac valve was pegged at 17% and it was just installed. I could only get the idle down to 689 without the iac plugged in but it helped the high idle. The pcm seems to be controlling the iac until I snap the throttle and then it drops back to 17% for a few minutes then goes back up between 24 and 30. What I have found is that the gem/body module is back feeding 3.6v to the clutch switch radio and ignition switch with low current because when I apply a test light from ground it pulls the voltage to ground instead of lighting. Also when I scoped the iac and tps to see if there was any correlation between those and the loss of iac control after the throttle snap I saw the tps 5v control and 5v circuits being pulled to ground intermittently. Out of curiosity I started checking random signal and reference wires all over and they all have the same spike to ground. I backporbed the 5vref at the pcm and saw the same spike with car running and a steady 5v with koeo. My assumption is that whatever is backfeeding the 3.6v from the gem is causing this issue is not allowing the pcm to see true values from the engine controls, or that same circuit isn't being backfed but rather its supposed to be 5v and is being pulled to ground because I notice it goes away with the clutch pedal depressed causing the same issue. I cannot find any good info on the clutch pedal values, and I cut the wire to the pedal and ignition switch and the 3.6v was still there until I unpluged the gem. From what I understand they should only read voltage with the key in the start position. I will attach a scope shot of the 5vref at pcm with iac, 5vref is yellow and iac purple. Any thoughts would be greatly appreciated.

so is the p0171 still in memory? the post is kind of confusing...

The kam has been erased but the fuel trims have shown the lean condition still, I think I am close to a resolution, the drops in the 5vref correlate with the spark spike. I'm leaning towards bad injector for the lean condition.I can't explain the spark line matching the drop on the 5vref. Here are some new shots. I believe the problem in the gem might be an effect not a cause. My most pressing concern is why the throttle snap causes the iac to drop to minimum for 10 minutes and why some of the scan data values don't seem to add up, like ect never reaching past186F. It has no coolant leaks and a new thermostat and thermostat housing

when are the trims high? idle or under load? does the maf sensor go above 4.0 volts when the throttle is snapped? fuel pressure in spec?

Fuel trims are high at idle, they drop to around a total of +20 to +25 between the LT and ST with the throttle snap, I believe one of the injectors is bad per 1 of the ignition waveforms I posted. I have repaired all of the vacuum leaks, diagnosed with smoke machine. This was previously a fleet vehicle, I've found quite a few electrical repairs and this is one of those Rangers that has 2 plugs for every cylinder. I believe my main concern now is that the 5vref along with some sensor feeds and control circuits get pulled to ground every time a coil collapses. My guess is that this is what is causing the iac to stop operating every time I snap the throttle. The customer replaced the tps, iac, maf, dpfe, power steering pressure switch, before bringing it to me trying to solve the idle problem. Once I set the minimum idle it is fine until throttle is snapped and I believe the circuits being pulled to ground is creating not such accurate scan data. Maf and fuel pressure are fine, new pump and filter as well. I believe it's time to check for injector balance and shorts in the ignition system. The last 2 pictures I posted were the 5vref (yellow ), ect sender (purple ), one of the 2 plug wires for cylinder 3 (blue). Thanks for the responses, I'm trying to attack the iac becoming erratic after throttle snap. All the basics have been checked, maf, tps response and v is .75 at idle and it rises on scan data with snap but on the waveform it gets pulled to ground when the coil collapses. I'm using a solus ultra. All the sensors show that drop( ground spike ) in the control, 5vref, or feed, or on sensor ground they show a positive spike when there is a positive firing coil collapse (2 coilpacks, 2 plugs per cylinder, waste spark ignition system