I don't think towing would put water in the engine like you had. The impeller would prevent any water from getting past it without it turning. Just not possible by design.
There had to be a way the water got there and the exhaust/cooling interface is the culprit 95% of the time. If you don't verify the exhaust sysem in not compromised. A bellows will not do it. A drive bellows will ruin your gimbal bearing and universals. An exhaust bellows is optional. My friend has a Regal 19 " bowrider that doesn't use a exhuast bellows.
It almost has to be:
1. Dieseling on the engine (AKA running backwards for a second or two)
2. A leaking exhaust elbow
3. A leaking exhaust manifold
4. A leaking/compromised gasket on the exhaust manifold, exhaust elbow or head.
5. A non-working vacumn break. See part 27 below.
6. Coming off plane real fast or going in reverse at a quick forward speed.
If you boat in fresh water only chances are your exhaust manifolds are fine. If you boat in saltwater even part of the time, the parts need to be checked or replaced.
Look at the point where your exhaust elbow and exhaust manifold mate, Part# 19. If you see any stains trailing from the joint you have a gasket issue for sure.
I'm guessing that you have a compromise. While the engine was running, exhaust pressure and heat kept the water out (small leak). You stopped, no more exhaust pressure and while it was sitting the water entered the exhaust gas passages and found it's way into the cylinder/cylinders where the valves were in the open position. So, you go to start it and it seems like a low battery because the water in the cylinders can't be compressed and has now fouled the plugs preventing any spark.
It may have been a one time incident but if it were me, I would definitely want to check everything out as the next time you may end up needing a new engine! Hydrolocks are UGLY and most of the time a knife in the heart of any motor. Some of your time and a couple hundred buck in parts vs. $4000 for a new long block and the labor to replace. Most of this is stuff that is relatively easy to do. Exhaust elbows are a piece of cake. The hardest part of the job can be getting the old many times corroded bolts off. If you want to try it, PM me and I'll list the steps I followed.
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Jvalich
http://www.badcock.com'04 FW 288 Vista "Mental Floss"