I had the same problem with my last engine, the problem went away
without touching the transmission.  I did get a new clutch and all of
the rotating parts balanced, including the new clutch, new pressure
plate and resurfaced flywheel.  I would start by checking the clutch,
pressure plate and flywheel.

David Filcoff            dave@v-dub.musa.com
Volkswagens!            http://v-dub.musa.com
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87 Vanagon, 88 Fox
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St. Louis / Columbia, MO
LiMBO - Gateway VW Club - VWoA VW Club -  Missouri Micros