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If you are careful during the 'decanting' of the water from the bowl of the Racor ... by s-l-o-w bleeding of water, you probably wont get any air into the system. Id fill the tank with a few gallons of diesel (get it from a truckstop as its usually fresher/drier) so that the 'siphon' effect from the tank into the Racor is 'better'.
If you need to bleed the system, start with the Racor (bleed screw on the Racor housing, sometimes depending on the Racor 'head' you will have a priming pump to aid bleeding, then bleed the 'guard' filter that mounted on the engine (has bleed screw) using the priming pump on the Racor to clear the air from the 'guard' filter. If the engine mounted 'lift pump' delivers TO the engine 'guard' filter then use the 'bail' on the lift pump to manually work the diaphargm of the lift pump to fill/purge air from the 'guard' filter.
Usually on Yamars all you have to bleed is the filters as they will usually start right up after you bleed the 'fuel delivery' lines. Rarely do you have to bleed the high pressure pump and the injectors --- thank you Mr. Yanmar !!!!
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