I would check out a) all vacuum pipes from your intake manifold for cracks etc. b) fuel pressure regulator (FPR) valve and your ignition coil. The function of these last two is not overseen by the engine ECU and if they are not behaving then you are the best diagnostic. Any small air leak into a vacuum pipe will compromise the intake manifold pressure management and the car will run roughy. The FPR is a small metal circular device and sits on the fuel rail; it has a vacuum pipe attached to it. Sometimes if the FPR is failing there smell of fuel from the vacuum arm when disconnecting the small diameter vacuum pipe. If the FPR leaks it makes the engine run richer than it should and the consequence is the ECU then alters the engine management to cope. This can lead to non-fire events and occasionally miss-fire as the engine goes from rich to lean and back again: basically mirroring the same events as with the cracked vacuum piping (above). Finally check that you are getting a good consistent spark on all plugs. Now check the resistance of each spark plug lead, they should all have high resistance but anything that looks extreme, compared to the rest, should be replaced. Remove the coil and give it a really good inspection, check for any cracks or obvious signs of shorts. Sometimes an intermittent short in the low tension coil side is really hard to detect but it will give rise to non-fire events. I keep stressing 'non-fire events' (or failure to fire) as miss-fire (out of time firing)) is often detected by the knock sensor etc.
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