I suspect something malfunctioning in water pickup. However, perhaps this has been discussed, but is boat salt water used/stored? It is my understanding that fresh water boat risers and exhaust manifolds don't clog up with rusts as frequent as salt water ones do. I have replaced several salt water manifolds/risers over my lifetime. Before you tear apart everything, with motor not running, you might want to disconnect plumbing at riser/manifold and hand connect a garden hose and see if there is any restrictions. If there is, you will get spray back in your face. I also had to replace water passage tube/seals in an Alpha one time and notice that there was too much corrosion to make a good seal. If my old memory serves me correctly, I had to replace upper unit. Good luck!
For the Alpha One yes, the water pocket cover was a problem area. But OP has a 1999, that makes it a Gen II, no water pocket covers in Gen IIs...
Consider yourself corrected... When you stop an engine, often as it comes to rest it gives a 'kick' the other way. That's enough to flick some or all of the blades the other way. The next time the engine is started, they flick back to other way...
Interesting.
the impeller acts like a vacuum, unless it's spinning and forcing water past it and through the system, it will act like a closed door.
