Has zero to do with your HPFP. You have an injector on bank two that is not metering correctly once in boost. Very common on these motors. Your log shows exactly that. Your Rail pressure is not "tanking" as some people are saying. If you also had a log of the FCV voltage you would see the rail pressure is dropping there because the DME is telling it to do so. When you come into boost look at your AFR's they both drop to 10:1 most likely due to an overaggressive PI map at boost onset. The DME tries to correct it by dropping rail pressure as well as other things. Bank 1 AFR recovers fine as the DME dials back fuel, but bank 2 stays rich in the 10's this is because your injector is dumping a bunch of fuel it isn't supposed to. The DME sees this rich condition and tries to correct it by dialing back fuel again, but it can only do so much, you get fuel trims out of whack, and a super-rich AFR on bank 2. These cars will actually run ok lean, if you run them rich they misfire immediately. Get a new set of injectors in the car, your problem will go away.
Does JB4 have some backwards logic I am missing? Do positive trims with JB4 mean that the dme is taking fuel away? Does TRIMS2 correlate with AFR1??? That would make more sense since "0" trims supposedly means -33%? Trims1 is 0 while AFR2 is reading rich.
datazap.me
Rail pressure IS tanking. Looks like wheelspin now that I look at the log again. 2nd gear with rpms jumping causing boost to spike to 20psi+ and rail pressure to drop. You're picking out a rich point in the log after boost is already falling again and the HPFP is already recovering (he's starting to hook back up). Maybe it is pid related, maybe it isn't, but the low rail pressure could definitely induce misfires. I know you n54 owners like to think it's ok to run low rail pressure...
AFR2 doesn't stay rich either... it actually leans back out to about 13:1 @ 5100rpm before enriching to 10.8:1 @5800rpm. STFT is pretty much +20 across that rpm range. Fuel trims are positive the entire pull. That doesn't align with leaky injectors dumping more fuel then they are supposed to. AFR1 seems to be behaving the way it's supposed to in-line with TRIMS1.
You mentioned port injection, but, i didn't see anywhere where he said he was running port injection? I do see OP made a post selling a port injection kit though...
datazap.me
Looking at the second log, with 3rd gear in isolation, there seems to be a few artifacts in the data. JB4 errors? FP_L reads out at "7" early on and then later AFR reads out as ".1". is this normal JB4 behavior lol? Log looks more normal with no wheel spin... AFR looks much better. Trims are positive but that's normal for a JB4 car running more boost or ethanol than the base map is dialed in for.
I wonder exactly where OP is having misfires? During wheelspin in 2nd gear where boost is spiking and HPFP is tanking? Some other specific place in the logs he posted?