My 2000 beetle runs very rough when I first start it up. Sometimes it will continue to miss and if I put it in drive it doesn't have enough power to move. Other times, after a few minutes of running very rough it will suddenly come to life and run great.

check fuel pump.if there is a small , even hairline crack in the diaphram it will do as yours does. good luck.

With the car running rough it could cause the harsh shift but if it is staying at 5000 rpms then the ****** is about to go out on you. The rough idle sounds like a vacuum leak. If you can keep the car running at idle listen for a sucking type sound. That would indicate where the vacuum leak is.

I would suggest you run a compression check on this engine and also have the coolant recovery tank tested for the presence of combustion gases with a gas analyzer, any gases would indicate a leaking head gasket. Any engine cylinder that is lower than 5% of the highest reading cylinder in pounds per square inch has a problem like a scored cylinder or leaking intake or exhaust valve seat.

without putting my machine on it and extracting the gas to see how much gas their is by weight then i couldnt even think of a reason for this sorry

make sure the car is fully in park! My mother does this all the time and just barely misses putting it in park just enough so the car doesn't start

Could be the fast idle sensor check to see that the vacume line is hooked up properly.

maybe coil pac!!!

I had that problem for the longest time. I had to clean the Mass Air Flow Sensor. Very easy to get to. Go to any auto parts store and ask them for the MAFS Spray. If cleaning it doesn't work, you may need to replace the MAFS. Once again easy to replace. Make sure you put it back nice and tight.....

could be a dry joint at fuel pump relay .open relyay up and check for dry loose joint then resolder dry joint and try again

most auto parts stores offer a "free scan" -your car has a prob,it can ONLY be found by scanning it(dont hesitate!!)