I have the same problem with my 2000 speedster. However, after a lot of blood pressure to the braqin from being upsidedown I have figured it out. The seal around the exhausts seems to have deteriorated somewhat and there is a slight trickle of water making its way in at the water line when the boat is out and about or standing still. Over the course of a couple of hours this would fill the engine compartment to just below the engine base which would let water run for several minutes when recovering. This water of course can move to the front of the boat too. I would try checking areas like that out first before I would consider something sinister with the engine etc
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