usdart, I have had a very similar issue with the Mopar boxs in the same instance. My biggest single best working idea so far was to rid myself of the MSD period. My luck has been terrible to say the least, but back to what I was saying.
When I wired in both systems, MoPar box upgrade first followed by the MSD, or MSD box with the stock wireing ignition there first, the switch over back to the Mopar ignition needed to be tweaked in timing a tad to get it just so. They need there own set point to work best.
I gotta agree with Don and state it over again here. The MSD will "Band-Aid" patch a weakness in the car from start to finish or air cleaner to tail pipe.
If you can dial in a car right without it and get the car running great , the MSD will be nice, not a band aid.
