Super tuning car runs good shooting for great

I have to wonder if it is:
- A grounding issue
- The MSD is looking for the polarity of the reluctor pulse to be inverted and is presently triggering off of the wrong pulse edge (the slow, falling edge of the pulse)
- Or your timing light is responding to different pulses in each set of sparks. I.e., it triggers off of spark #1 for one cylinder, then triggers off of spark #2 or #3 in the next cylinder's set of sparks. I think MSD has some tech info on timing lights on their site.

Good points here. I have first hand experience with the polarity issue but it was with the pickup wires specifically. I could not get the car to start after installing an MSD 6A and went on Moparts asking for help. Someone suggested I switch the polarity of the pickup wires. I did and it fired right up without hesitation and ran great.

Dial back timing lights are not supposed to work with MSD ignitions. My old regular Sears one is fine with it though.

I would also say that in no universe is a Mopar orange box a better ignition controller than an MSD. It might run better right now with the orange box because the electronics in it probably won't pick up more subtle issues like you're having but once you get to the root of your issue, the MSD will be a better choice.