last weekend i finished rebuilding the engine in my gti,i fired it up and its running and sounds good.the only problem i am having is that im getting a misfire on cylinder #6(p0306). i also get an occasional random/multiple cylinder misfire(p0300),only under heavy acceleration and until the enigne reaches about 4000rpm. i have replaced the spark plugs, the spark plug wires, and also tried switching the injectors,still without any luck.

 

Check the ignition module, mine was cracked and caused the same symptoms you are describing. I fixed it with epoxy. I think what happens is that a short occurs through the module to the head. Also try looking at all the plug wires in the dark (with the engine running) to see if there is any arcing. It could be a bad wire. I had that problem as well.
Good luck.

 

Get a new coil pack, just replaced mine, all the stores have em for like $400 min, got mine off ebay for $200, but had to switch the plug from the original, it's only 2 screws. Trust me, it worked.