I know you've replaced it, but I've seen this caused by a defective
water pump impeller. Its really easy to ruin the Yanmar impeller - it
looks good but its seal is just bad enough that it likes to air lock.
Replacing the impeller on spec is a cheap experiment - if it fails you
have a spare :-) And make sure you put the new one in correctly, and
don't run it dry to start with.
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