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Did you have a P0300 code or did you have an individual misfire code for each of the six cylinders?
Have you ever been able to clear the codes driving a short distance until it starts to act up and stop and check the codes immediately to see if you can get any one particular cylinder misfire?
Okay, here's the bot***** *****ne. This engine was notorious to have bad ignition coil issues. It is possible that one ignition quote could be failing and if it fails on the IGF for confirmation feedback signal side it will intermittently take down all six coils at any one given time. There is an IGT or trigger signal sent to the coil and IGF confirmation signal sent from and to the computer. The IGF signal shares a common line between all six coils. If you're planning on keeping the car long-term I usually recommend replacing all six ignition coils if you cannot isolate whitch cylinder it is. Use only DENSO brand ignition coils rock auto.com has about the best price on these. Do not use cheap ignition coils they will be a problem and the back bank by the firewall has to have the upper intake Plenum removed in order to replace those three. If you are patient and have a scan tool readily attached to the vehicle while driving ideally when the problem occurs run a check of the codes and see if you can isolate which the cylinders might be causing the problem. Please not forget to rate the assistance that I provided you at three or higher and any bonus is greatly appreciated. If you need any additional input feel free to reply and I will get back to you.