Ski filled with water. HELP

My son was riding with a friend this weekend and came flying back to the dock to say that our modded ski was dead. We quickly ran out to it and towed it back. When we got it on the lift and pulled the hood the whole hull was filled and the cap on the hood was popped off. Honestly I don't know how it didn't sink. I tipped it over to drain the water and it fired right up but the electric bilge isnt pumping and the exhaust had blown apart at the rubber boot. It has a side exhaust. I am not even sure where to start with figuring out what caused all of this or how far I have to tear everything down to prevent further issues from being flooded. Any advice is appreciated.
 
Overview of the hull, Ehaust popped apart and bilge. My son informed me that he had to start it with the booster box but it was reading 13.8 volts while running so I am thinking maybe with the bad or dead battery the stator doesn't have the amperage needed to run the bilge fast enough but still don't understand why the exhaust popped apart like this.
 

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WFO Speedracer

A lifetime ban is like a lifetime warranty !
Location
Alabama
You need to take the exhaust apart and inspect the rubber boot really well, keep in mind they stopped making 650SX's back in the ninties so those exhaust couplers are now 25 -30 years old, if everything looks good , clean it well reassemble it and tighten the clamps, rubber part deteorite, clamps loosen over time etc, One more thing if skis didn't break I wouldn't have a job .
 
The Exhaust Chamber Halves have to mate flush and square with no gaps.

Clean and degrease the Chamber Sections and the Rubber Coupler with soapy water.

To verify, minus the Coupling so you can see, rotate the last Chamber section until it mates/butts square with the other Section.

With a Sharpie, make an alignment mark on both Chamber Sections for reference.

Also put the Coupler on top of the two mated Chamber Sections and mark where the Coupler Ends will be when the Pipe is fitted correctly with the Coupler.

Now install the Coupler with soapy water and mate the Exhaust Sections using the Sharpie Marks for reference.

Tighten the Hose Clamps well but not so much to where it cuts into the Coupler.

By the way, I think the original Clamps had rolled edges to allow for a high clamping load without cutting into the Rubber Coupling.
Do I need to worry about water in the case or anything like that? I ordered a new battery and will verify the bilge is functioning before taking out again. I would say this one has 3-4 times the power our stock 650 has. I wish I knew what was done to it.
 
It definitely is that! It have with half of a rooster shooter set up still on it, missing the moving parts. That caused it to porpoise really bad. Now that we have a stock nozzle it handles much better. My sons rarely ever ride our seadoos anymore and are wanting to tear the stock one apart for mods. I guess I taught them well. Lol
3 to 4 times the Power o_O? maybe 20-40% more HP, from Porting, Compression, Timing Advance, Impeller and maybe Light Flywheel. Acceleration and Top Speed are two different things... Doesn't really matter as long as it's fun to ride.

After an Engine flooding event, supposed to drain all the Water out, get the Engine running and immediately ride the Ski for a good 30 minutes to dry out the Engine and lubricate the Internal Parts, especially the Bearings.
 
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