Are all 4 injection pump mounting bolts tight? If you forgot about the back one it will cause vibes like you are describing.
Tapered nut: 068130197 ; 068130143$4.27http://www.jimellisvwparts.com/products/Volkswagen-VW/1986/Jetta16L-TD5-MT/Tapered-nut/5140968/068130197.html(You might need the bushing too.)
^ Ja, the harmonics are wicked. They prolly interfere with the swing of the governor weights, causing movement that shifts the control collar. As for the bushing, it is like the bushing for the alternator bracket, but it has the tapered recess to fit the nut. It is usually trapped by the IP, but check for it being there, just in case...