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I have a yanmar 3gmd and encountered a similar plroblem after changing my fuel filters. My engine seems to get little air bubles stuck in the high pressure fuel lines.
When using your manual fuel pump to bleed the injecters, make sure you are at full throttle, those little manual pumps need all the help they can get in order to pump enough fuel to get out all the air.
Also, depending on how long ago you changed your filters, you may have nocked loose some gunk into your injectors. Good luck
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