If I were me I'd pull that thing apart if you are looking to use it for moving a boat. What's the underwater pressure rating for that engine?
I can't even really speculate on where the water may have gotten to other than everywhere. Don't know much about that particular engine (nothing actually) but is it electronically controlled or mechanical? Did water get into the injection pump and lock it up? If you start it up and it is knocking like a MF have you already done some damage?
If you do start it up pull the glow plugs and/or injectors and crank it over then let it sit for a day or two then reassemble, crack all the injector lines till you get flow out of each one and that will give the cylinders time to purge most of the remaining water. It will also tell you if your IP is doing its job. then tighten the lines and pray. You need fuel
(crack inj lines til it flows), compression
to maintain min RPM
for starting) and air (make sure intake isn't full of debris). If it is electronically controled there is alot more to it, (I don't think it is).