Here is a Yamaha guys' interpretation of this request.
My older 2-stroke Yamaha sleds were twin and triple cylinder liquid cooled engines. My first Yamaha Waverunners were derivitives of this engine with tons of modifications to make them cool from lake water. Of course no transmission was used as it was a direct drive to the impeller. I would guess mounting them in a PWC would require more shock protection, but the sled mount did that as well.
My new 4-stroke Yamaha sled is a 4-cyl liquid cooled 1000cc engine derived from the Yamaha R1 motorcycle. Near identical in fact. There again, no transmission as the sled uses the CVT clutches to drive the track. Liquid cooling remained sealed in the sled, like the bike. A derivitive of that engine is now used in the Yamaha PWC and boats. There again, the cooling system modified to use lake water instead of being sealed. This would be a huge undertaking in anyone's personal shop. One would do it just to say they did it, and not for any practical purposes at all, as we all know what the practical solution would be.
Yamaha is first off, an engine company. They will do what they can to utilize their proven engines in as many forms as they can. This conversation is coming up on Yamaha Sled boards and Arctic cat sled boards as there is specualtion that Yamaha could be selling engines to Arctic cat in the near future. Arctic recently cut thier long ties with Suzuki for engines.
So, it can be done, (minus trans and possibly cooling) and I would take some serious notes from a Honda Aquatrax to find similarities to your project. But the questions above were GOLD:
1. How familiar are you with Jet Theory
2. How good are you with fiberglass.