The fix for this is easy... Replace the coil packs... Like in any car, they eventually wear out and cause misfires. The dealer has the newest "revision", they should run about 30-50 each (from the dealer, probably cheaper online). Simple pop-in, pop-out replacement... Takes about 10 mins.I believe there is a coil pack problem. I'm not sure if it's for all MK4s but I do know my 01 does it. Random miss-fire. Every 1000 miles i get this miss-fire for like 70 miles. The car won't run properly, it bucks, and i can't accelerate.. and rpms jump everywhere.
**Now to answer some of the OPs questions...
1) Depending on the year of the Jetta, it should be very similar to the 2001-2004 Audi TT (same engine code). There was a shift in the motors in the Jetta in 2002 (mostly programing). Look for a later model one (2002+) AWP engine code is the stronger one for the Jetta.
A) I believe so... I haven't hit that mileage, but from what I understand you should replace the timing belt and the waterpump (or part thereof) at about 65000 in order to prevent issues.
2) It seems that all inherant problems have relitivly simple fixes, and with good mantience can be mostly avoided. The most that I hear abour are the coil packs (simple fix - replace), and the timing belt. if you are going to heavily mod the car though, there could be other issues that pop up as a result.
3) They are a lot of fun and there is a ton you can do with them on the aftermarket (if that's what you're in to). So far mine has been quite reliable and a blast to drive. Some say that the VR6 is more reliable than the 1.8T, but this is subjective becasue the 1.8 has the turbo. The 2.0L can be quite sluggish as times, but are great on gas mileage (although the 1.8T have a higher EPA mileage rating). Any way you look at it, I think they are awesome cars...
FYI - More info on the 1.8T engine can be found here: http://forums.vwvortex.com/zerothread?id=2666114