So here is where we are at currently. The taillight was replaced with a new unit, the headlight wiring was replaced with new adapter harnesses, and the dealer pinpointed an issue with the power feed going to the IPDC (Same part that was replaced back in August). They also found a couple of blown fuses that are related to modules controlled by the IPDC. All of that was corrected. Check engine/warning lights were cleared and the codes have not returned. Dealer took the vehicle on an extended test drive, and I have put another 30-40 miles on it after and as of right now (knocking on wood as I type this) it is running like a dream.
The technician's thoughts: He specializes in electrical related repairs for this particular dealer. He obviously doesn't know for certain, but he believes the collection of water inside the taillight did result in some of the other bizarre issues I was seeing. He also said it may have caused the failure in the Retroshop adapter harnesses as most of the truck's exterior lighting is all tied together in some fashion, so there is a good chance that is what fried the harness. The fuse tap from the Retroshop adapter that provides power to the OEM headlight DRL's was linked with all of the other modules with the IPDC that was also experiencing issues. The blown fuses that they found could have resulted from that since everything was sort of tied in with each other. Is this accurate? Who knows, but I can certainly follow along with how he connected the dots and made it all come back full circle.
I'm not sure if the synopsis above is correct or not, but I thought for certain they were going to charge me this time around since they had reason to believe that an aftermarket component did have some bearing to the problem. Even if the root cause was water related from the taillight failure. They didn't charge me a penny though. The service advisor reassured me before I left that if any of the issues return, to bring it right back in so they can keep digging, but that they both think this should hopefully be the end of it. We will see!
Side note: I really hope this is the last time I have to rip the front end of the truck apart for awhile