have a 1990 formula with the silent thunder exhaust that comes thru the platform

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recently we replaced the seized 454 engine, while initial start-up attemped, the engine backfired, and the back platform u-bolt fell off, from a combination of rusted bolt / backfire explosion, the bolt was replaced with new, the boat was launched, and ran, ran excellent, after about an hour at about 2000 rpm, the engine stopped, and will not crank over , like there's water in the cylinders, could the flatform have anything to do with the possibility of water entering the cylinders, the boat has a silent thunder patent #4744778, any help would be greatly appreciated, thanks