That may be where your problem is at. Did you check to see if throw out bearing was centered on pressure plate (without trans installed)? I had that problem with my Quick Time bellhousing, see my thread on my install: http://www.forabodiesonly.com/mopar/showthread.php?t=60549;
go to post #5. If the clutch fork and pivot bracket are not correct it can force the throw out bearing out of alignment when you push the clutch.