Have you changed the plugs and wires? Could the the coil too. Thats what misfire usually points to.
What about fueling issues? Fuel filter? Def. try a new MAF.
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The Baby: Darla, 102k, '99 New Beetle GL 5-speed. Bone stock. Acquired 4/6/05. Gave her life for me 8/17/11. RIP 
The Project: Klaus, 180k+, '84 Jetta GL Turbo Diesel. Rebuilt and bringing 50+ mpg. Slightly improved from stock  Acquired 7/12/08
The Baby Brother: Günther, 20th Anniversary Edition GTI 
The money saver: 2001 Jetta TDI GL. 114k. Dead auto, swapped to 3 pedals. Hubby's DD and our trip car
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