Exactly how bad are the flappers? Pics would be great.
Also, how hot was the overheat? Where was the temp gauge.
A hot engine won't just suck water up the exhausts into the manifolds and cylinders, but the flappers do serve a purpose. There are two main way water can be forced up the exhaust and into the cylinders. First, if while stopped you catch a big wave to the transom with the engine off, the wave can travel up the exhaust pipes into the center of the riser and down into the manifolds to the exhaust valves. Second, if the engine is shut off while the boat is up on plane without idling down first, the trailing wave that forms behind the boat will crash into the transom. Without flappers or engine exhaust to stop it, this wave will also travel up the exhaust pipes and into the manifolds. Flappers in good condition protect the engine in both of these scenarios.
Also if the manifold do get flooded, the engine doesn't immediately lock up because only a couple of exhaust valves are open at any one time. But once the water it in the manifold, it will sit in the runners until the exhaust valve opens. It would take one or two turns of the engine, just as you described, for all the valves to have opened and completely lock the engine up.
Does either of the two situations fit you? Flapper condition is critical here. We NEED to know how bad they are.
I would get some sort of oil into those cylinders pronto to keep the cylinder walls and rings from rusting. Also check the oil for water contamination. You will want to change it before running it again anyway.
I really don't think you burned though the riser gasket. It is made of some pretty resilient stuff. It seemed almost like lead when I scraped it off the last time I had my risers off. I'm pretty sure if you got it hot enough to burn through that gasket, it would cook the exhaust hoses on the manifolds. You'd know it if you did that, those hoses smoke and stink when they start to melt.
1992 Supra Mariah - Red
PCM 351HO 285hp - PCM 1.23:1 Transmission
OJ XMP 4 Blade CNC 13x15.5RH
"People do weird things to boats" -Unknown