This will probably catch some crap, but the "running the motor dry" on a jetboat to evacuate water in the passages is pretty useless. For one, there is no water pump to push the water out, so once the pump is unloaded the flow of water is going to stop, and water will settle to any low point below the outlet for the cooling system. Any vacum the exiting exhaust is going to pull won't have a snowballs chance and pulling water up and over the snails, let alone out of the block. The only thing "drying out the pipes" does is allow guys with OTs to purge the last little bit of water out of the bend in the primaries on the headers so they don't rust out from the inside; or so the motor doesn't take a gulp water if the water didn't evaporate before you went to start it again.
If you don't believe me on this, take the pepsi challenge next time you get your boat out of the water. Feel free to rev the piss out of it on the ramp after you pull it out. Then when the boat is on level ground, pull one of the cooling hoses running to the bottom of the log or the drain plugs if your logs are so equipped. There will be water that drains out of it. If your logs aren't setup with a bung/fitting in front of the elbow, pull one of the drain plugs on the block; either way, you'll get some water out of the thing. Trust me, I drain my lightnings after every trip because there is water left in the jackets that would otherwise sit there with nothing to do but foul things up.
With aluminum manifolds, it doesn't take long to heat things up to the point where surfaces can get distorted. By the time you got stuff hot enough to boil the standing water out of the exhaust and block, you'd have bigger problems to worry about.
The next issue is that running the thing dry for 30 seconds every time you pull the boat out of the water will reduce the life of your wear ring to impeller clearance. While we can most definitely debate how much it degrades the clearance, you can't ignore the fact that it does cause premature wear on a tight pump.
Glad you found the true culprit for the problem, and hopefully the rest of the motor is an oil change and gaskets away from running well.