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
Found a massive leak!
Water is coming from the joint where the top part of the boat is glued to the bottom part (the fiberglass joint that runs under the black rubber bumpers). The bumper is riveted to the fiberglass. It’s possible that the leak is from the rivets but the leak is so massive I think the seam between the two half’s of the boat has come apart. The leak only occurs when the swim platform is summered (while launching the boat or at speed when the back end gets below water line). I was only able to see this leak by following the suggestions on this forum. I did have to take the “hood” (engine cover off to get to see exatally where the leak was at and the leak ran along the joint that is clued to hold the bottom and the top of the boat. Anyone have this issue? If so, how to fix it?