I don't remember you saying anything about surging or running bad when this began, I was not convinced it was a drive line issue from the description, it still may be part of the problem, so let's get the engine straight first. I would go through the surging idle checklist.
Replace the motor mounts, you did say they were suspect.
Everything starts with the engine, literally, if it ain't right, nothing is right.
DISCLAIMER: this is an opinion based on what I read, and my reading is suspect at best, not based on any real mechanical experience.