Alright - I FINALLY got my machine back on Thursday. I reluctantly ended up taking it back to the dealer after doing all the previously mentioned troubleshooting since I had to go away for work and wanted it resolved. After studying the electrical drawings and reading up on fuel injection I kept coming back to the PCM as the only logical thing that could cause the issue in one cylinder and not the other - all the input sensors that the PCM uses to calculate a outputs are common so there was no reason a bad sensor would only impact one. It seemed to me that one injector was getting a signal for full pulse width while the other was getting the correct signal. At one point over a month back I called and got a quote on a new PCM but asked them to connect their diagnostic tool and compare injector pulse width for both cylinders at idle and see what the PCM was doing. There was a lot of back and forth on this and I never actually got a clear answer that they actually did as I requested but they ended up taking another Pioneer of the same year in on trade and tried swapping PCMs. The problem immediately went away and would return when the original was reinstalled. Once this was confirmed, a new replacement was ordered, installed and I am finally back on the trail - needless to say my tires are back on and the tracks were spared a season of wear and tear.
The only reasonable explanation I can come up with is that the PCM was somehow damaged due to a short, or surge, while the machine was jump started since the starting battery was bad and did not get replaced to begin with. I am a bit surprised that a code was never thrown due to the deviation. I do think it should have been pretty apparent when viewing the system live through a diagnostic tool but without ever seeing this for a pioneer its hard for me to say.
I really appreciate the feedback and troubleshooting support that everyone has provided - I am not sure how likely it is that anyone else encounters this same scenario but if they do, I hope this thread will help them to have considerably less down time than I had!
