Figured I'd close out this thread...
BoostedTech has driven around with my supercharger on their Jeep for the last week and has not found any issues with it.
I've also been driving around with my engine and transmission for the last week and put on 500 miles and have not found any issues with those other than possibly a slow shift from 3rd to 4th.
Hopefully if anyone has this problem in the future and finds this thread you'll have better luck diagnosing than I had... Post up the solution if you find it.