I have a Pfaff 2038 with issues also. From the day it was new, it has been tempermental and will clunk and stop sewing at least once a year. It hates C&C thread. My daugther bought the same machine from the same dealer at about the same time and has never had an issue.
When it is working it is so wonderful. It is now needing a fix again. So this time I went and bought a Pfaff Ambition (a very very very nice machine for the money.) I am conflicted about fixing my old friend one more time. Another $100 bucks to fix the timing. (I do have a Viking and a Kenmore back up machines.) It does sound suspiciously like the same problem you had and could posibly need the same fix. $450 though - mine was new in 2001. Maybe next year.