Just diagnosed this on our 2001 this weekend - wife called Thursday night and thought there was something wrong with the transmission (I thought maybe rear diff or possible transfer case, doh), odd vibration/drivetrain roughness taking off from and coming to a stop, with other intermittent roughness. I drove it a couple times around the block and found it disappeared after the truck warmed up, but no apparent relationship to speed, or 4Lo/Hi or locked centre diff, other than the starting and stopping. Came out an hour later (after some dinner) to pop out to the local drug store and noticed an idle dip/rough idle as soon as I dropped it into reverse, pop it back into park and it high idled and went away, into reverse and same thing, gone by the time I left the drug store to come home - having experienced a coil pack failure on our 4 cylinder turbo Passat, I knew the symptoms immediately. Drove it to work the next day and it was intermittently misfiring like crazy.
Phoned around and could only find jobber replacements (and $105 Cdn vs. $176 at the dealer delivered the following week). It took me longer to get my code reader to work with my ipod than it did to replace the coil - P305.
Someone said in another thread check #5 cylinder first.
Thanks again for assembling this FAQ.
John