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Hello. I bought the above machine in non-running condition at an auction and do not know much about its history. 136 hours and in excellent cosmetic condition. Oil in the tank is clean. Plugs looked good. Pulled the plugs and discovered salt water in the cylinder closest to the rear of the machine which I withdrew. Sprayed PB Blaster and then Sea Foam Deep Creep into all of the cylinders and let it sit for a few days. I put a new gsm battery in it and everything powers up including the fuel pump. When I push the start button, the starter makes a clunking type noise but will not turn the engine over. I put a chain wrench around the coupler and the engine still will not turn over even after exerting a medium amount of force. Looking for some thoughts about determining whether the engine is the problem, the jet pump is stuck or whether the starter/auxiliary gear are stuck against the flywheel. Any help is appreciated! Thanks, Bill.
 

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From sounds of things I'd say it's the motor. Don't forget with saltwater in the cyl the valves are probably frozen also, and could have water in the base and the crank is also frozen. That's to much for a starter to overcome. Not likely to be able to do with wrench either.
That being said, the pump could also be locked up to if the wear ring swelled up from salt corrosion.

Best bet would be to pull the motor and free items up and inspect as you disassemble. With the head off you could put a few tablespoons of transmission fluid (ATF) in each cyl. Then use a 2x4 or hammer handle to tap each Piston to work them free, maybe.
 

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We now know for sure Ski had been sunk and was why it was at auction and going cheap.

I would not try and force anything, buy a full gasket kit and pull the engine apart, once engine is out see if the jet pump spins freely.
If impeller and shaft all turn then all good with that.
As Dave said valves could be corroded as well as crank.
Much better over all to just disassemble and then clean everything properly see if rings need to be replaced, check bores, valves and rockers cleaned and oiled.
It must have been a great price considering it was a non working ski, so spending $500 to a $1000 to get it back to scratch should be worth it.
Starter sounds like it's ok as they are pretty water resistant being on the outside of the engine as is most of the other items around the engine.
Water does get inside the ski from flipping and the occasional broken hose or faulty hose clamp, mine nearly sank from a flush connection coming off, it's amazing how much water the Jet Pump can push through a half inch tube :)
I had water up to the top of the battery, the poor bilge had no chance of keeping that under control :), lucky I wasn't far from the Boat ramp when I realised it was taking on water :)
That was the third time I nearly sank my FX-SHO, twice from clamps, one rusted away as it wasn't a stainless steel one, even though I flushed and sprayed every time we went out in the salt.
Once a clamp not tightened after a service which allowed the flush port to pop off and a bad hose under the inlet manifold, that was a little more work to replace.
After the third time I got my mechanic to replace all the hose clamps and hoses.
Yamaha didn't use Stainless for it's hose clamps on the 2008 FX-SHO :(
You should have seen the condition of all the lower hose clamps, all in places you can't easily see or know they are there, so trying to spray them is nigh on impossible.
Once you have re-assembled the engine after replacing and cleaning everything, you will have a nice low hours Ski that will give you many hours of fun.
 
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