Well if it's not the pump it would have to be a mechanical problem with the engine, however the miss sounds to be intermittent. If there was a cylinder down on compression due to a ring issue or valve not sealing, the low compression would cause poor running consistently which typically will diminish as rpm increases as there is less time for the engine to loose compression. Have you done a leak down test? Another possible way to help with diagnosis would be to pull the injectors and inspect the tips of the nozzles. If there is a cylinder that is struggling to fire correctly the nozzle will be either moist with fuel or carbon'd up more than the other nozzles. Something to look at anyway. If you still can't narrow it down to a particular cylinder via injector inspection or a leak down test, I would suspect the pump and try swapping with another one.
Jason
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