The trailer plug or ground wire was the first thoughts I had too, so I unplugged all wiring at the harness connections (a 4 plug port near the spare tire) to clean and check. With all unplugged and the indicator on for a right turn, it still blinks the third brake light. This eliminates the trailer plug, and wiring/grounding issues on either tail lamp.
Chasing this down further, I have to agree with glkingar. Directional controls and tranfer case commands pass through the body control module. It also explains why my gear selector display is dim and not responsive sometimes, and the occasional dead passenger side door. Grounds have recently been cleaned and checked.
If this was not my daily driver, I'd park it and fix the small stuff. This isn't the only issue, but most things are very minor and common on a near 200K mile truck. But I need to get to work and job sites without fail. So I bought a new truck.
Thanks for all the help guys. I'll post a new thread about the new truck with photos, once I take delivery on Tuesday.