I actually discovered that the polarity is labeled backwards in the diagrams by accident. I installed the left dash & front door speakers first, and before replacing the original speakers on the right side to compare them. When I started playing music and turned up the volume, I could immediately tell the speakers were out-of-phase with each other. Specifically, the left speakers were out of phase with the right speakers. When you hear out-of-phase speakers once you don't forget how it sounds. Two speakers that are out of phase with each other sound quietest when positioned in the center between them. This is because the cancelling effect is greatest when listening with equal distance from both speakers. Each speaker will sound louder as you move your ears closer to it because the cancelling effect decreases as you move further from the other speaker. Obviously, the farther the speakers are apart the less audible this becomes, but in a confined space like your car it is usually very obvious.
Like I said before, I reversed the polarity of all my speaker wiring adapters ahead of time assuming the wiring information from the service manual,
Mopar's connector site, and Crutchfield's Mastersheet were correct because they all match each other. When I heard the new speakers were out-of-phase with the old ones, I thought it was impossible that all three sources could be wrong. I
connected a 9V battery to each factory speaker (bypassing the capacitor on the dash speakers) to test their polarity. Sure enough, my findings confirmed that, the wiring diagrams are have the polarity incorrectly labeled. The 2.2 uF capacitor on the dash speakers is also wired in series with the negative terminal instead of the positive terminal like they typically are. I removed the left speakers again, re-pinned all the wiring harnesses back to how they came from Metra, and reinstalled them. When I listened again, the speakers sounded correct and in phase with each other.
If you do some online research, you'll find that other FCA vehicle owners also discovered this same anomaly with their vehicles. Many of them use the exact same speakers (have same OEM part numbers) as the Pacifica, so this is very plausible.
I also confirmed with an ohmmeter that the like colored wires are in fact the same between the dash speakers and the door speakers. In the base six speaker system, the dash speakers are wired in parallel with the front door speakers. Knowing this, I felt it was necessary to ensure that Chrysler wired the dash speakers to be in phase with the door speakers and not out of phase.
Just to clarify, everything with the wiring diagrams is correct with regard to colors and numbering of terminal locations. The only thing that is wrong is the positive and negative labels are reversed on all the speakers - at least on vans with the base audio system. It's very possible that all vans are like this regardless of which audio system they came with. The Metra 72-7902 (for 3.5" speaker locations) and 72-6515 (for 6x9" speaker locations) speaker wiring adapters are correct and should be used as they come without altering them.
Normally, polarity doesn't actually matter as long as all your speakers are connected the same way so that they're in phase with each other. However, in a system with Active Noise Cancelling, if all the speakers are connected backwards the speakers will generate a sound that amplifies engine noise instead of cancelling it out as intended. So if you are hearing engine noise in the speakers, checking and/or reversing their polarity is a good place to start.
I can confirm that ANC is working fine at this point, so the front speakers I installed are wired correctly. No engine noise is audible from any of the speakers. At this point I'm assuming that the sliding door speakers are also labeled backwards in the wiring diagrams, because when comparing front to rear speakers, they sound in phase with each other. I will make observations when installing the new rear speakers and post what I find afterwards. I hope to get them in later today or tonight.
I hope others find this helpful because I was completely blindsided with this issue. I still find it hard to believe that three reputable sources of information were consistently wrong.
If you used the Metra 72-7902 adapters (and didn't alter them), your speakers should be wired correctly. I would first check your EQ settings. Center all the bands and see if it goes away. You should install a bass blocker/capacitor in series with your front speakers. This will filter the lower frequencies that they can't reproduce, which will reduce distortion. If your Jeep has a premium Alpine/HK system, the signal that is being fed to the front dash speakers already has a high-pass filter applied to it (same goes for a Pacifica's Alpine/HK system). This would explain the difference in sound between the two vehicles.
I haven't installed any sound deadening, but I might attempt it later. The carrier plate actually looks easy to remove, it's just dealing with the window regulator and door latch in the process that I find intimidating.