Alright....good talk. In case anybody is following this or can benefit from my ham-fisted attempt to fix this thing, here's an update: Since my last post I completely disassembled the shifter assembly, bought a new shift rod, adjusted the rearset geometry, adjusted shifter sensitivity, and still got no love. As I was manually shifting through the gears on the stand I noticed the display was skipping 3rd gear. It would go from 1 - N - 2 - 4 - 5 - 6. I pulled it off and attempted to manually put it in the 3rd gear position. It continued to skip 3rd gear. It's definitely f*cked. The Bazzaz troubleshooting algorithm also points to the Gear Position Sensor (GPS) as the suspected culprit. I have a new one on order which comes with the updated wiring harness. More to follow.
Mods: At this point I doubt this is an AP Rearset issue. Feel free to move this to the appropriate forum.