The shuttle shifts from 2nd, 3rd, 2nd, 3rd is a dead give away. The "shuttle shift" you are experiencing is a common issue, I remember reading a thread about it and how to correct it. Maybe someone else can chime in with more info. If not google "ram 46re shuttle shift".

 

Haha good point. I was thinking of the PCV valve.

Cylinders are clean. I seafoam a few times a year and when I was in the motor less than a year ago, I cleaned out all carbon from the combustion chamber.

I put in the new ignition parts this morning. Not many places where I can go WOT on my way to work (live in a city), but I got a short run in on one stretch and I think that might have solved my pinging issue. The cap had some corrosion and 2 wires had been burned pretty severely on a header.

 

I did a quick search for that, and will do some more digging. My trans is a reman unit that's about 2 years old that I installed a Transgo TFOD JR shift kit in. Shifts perfect when not tuned, but with the superchips tuning it does the "shuttle shift".