I unplugged the MAF and it died. Then I started it unplugged and it ran but still had the miss at idle so I didn't attempt to drive it unplugged.
Also noteworthy, I haven't had a CEL through any of this. Not even from the ORX (with no tune or MIL eliminators).
What you posted concerning min and max STFT/LTFT data isn't sufficient to make an informed diagnosis. You would need to evaluate a multitude of factors (PIDs) in real-time or via logs to determine what's going on.
Also, during WOT, the system is in open loop. During such, O2 sensors are not used to determine stoichiometric AFR. The PCM refers to preset tables. So you can ignore STFT/LTFT data during WOT. Also I would not recommend hard accelerations until your problem is resolved. Plus its easier to diagnose in closed loop w/ O2 sensor feedback.
With these cars, any time I've had a misfire, stumbling or hesitation issue its always been the wireset as the root cause. They can arc where you cannot visually see them, where the boot in inserted into the head. Have you attempted verifying that your wires are not arching. Pull them off one by one and look for anything abnormal. Take your time in doing so as the slightest hole can be easily over-looked, but lead to the very problem you're experiencing.
Another problem source would be the the fuel filter, but you're already replaced this.
Have you attempted cleaning your MAF?
Also you mentioned it was running fine before all the maintenance was performed. Did you put a Duralast wirelset on it? I've went through three "brand new" sets all with arching issues which presented as hesitation/misfiring before switching back to a FRPP set to resolve my issues. Would you happen to have the old wireset you could try?
You mentioned the fuel pump duty cycle was at 100%, I'm not positive we can log this on our cars. Maybe some else can chime in.
You can try a fuel system pressure test to see where you're at. You should be around ~32 psi with the FPR connected and ~42 psi with the FPR disconnected at idle, IIRC.
Regarding the possible leaking FPR, you would see this when datalogging. Abnormal STFT/LTFT values when it starts leaking and PCM tries to adjust for this. Also when it leaks O2B1S1 and/or O2B2S1 would read constantly high in voltage ( closer to 1.0V with 0.0V indicating lean and 1.0V indicating rich ). Normally O2B1S1 and O2B2S1 should be switching between 0.0V and 1.0V. This is also another way to determine if an O2 sensor is faulty.
For future reference, if you have a O2 sensor code reading lean. Look to these PIDs and see what they're doing. If they're not switching, then you've found a problem. You can also try to spray a shot of carb cleaner or something in the intake and watch those voltages, when you do they should rise closer to 1.0V. If the target sensor does not rise in voltage it is most likely faulty. Switching O2 sensors across bank 1 and datalogging while performing the above is also another effective tactic to verify your findings.