A well matched turbo can get very quick response with greater durability at the same sustained power output because you don't have to generate the extra cylinder pressure to produce all the power lost in driving a supercharger.
In my experience boats rarely require full throttle from a standing idle. they are normally at least at a fast idle when you nail it.
Most of my experience comes from circuit racing and ski racing.
With fully submerged propellers, I normally put the water scoop just behind the propeller and that way protect it to some degree from debris If you run legs that is probably not an option and a presume your pick up is built into the leg.
I run all water through several less critical to thermal shck devices before it goes into the block so as to preheat it somewhat.
I size the system to run at a maximum of 80 deg C under the most severe stable conditions.
I size the discharge side slightly smaller than the inlet so as to build some pressure and thereby avoid possible localised boiling ans build up of salt deposits.
I check water pressure in the head and never allow it to go over about 100 psi as it is then to inclined to leak past the gaskets and enter cylinders or the sump.
I would not pull to much vacuum on the crankcase on an endurance engine as it lowers the boiling point of the engine oil and can damage gudgeon pins. Enough to stop leaks and to eat up blowby, but not enough to suck in seals or gaskets and let the oil on the bottom side of the piston crown and the pin boil or lose it's lubrication capacity. It does help clean fuel and water contamination from the oil. Maybe 5 psi vacuum.
A dry sump might be value at the cost/benefit range you seem to explore. Even a single stage scavenge and the OEM pressure pump system can be a good gain. A 5 stage system costs a truckload more and gains only a little extra over a 3 stage.
I think best value is one pick up from the back corner (that is back of the boat) of the sump on the side the oil throws toward and one from the valley with all other returns from the valley blocked off is the best value.
With a positive displacement blower like a roots, you do not need high compression for response as the instantaneous boost builds effective compression in an instant.
With a centrifugal pump like a turbo, you do need reasonable compression to get response before boost builds.
With a twin charger, you can run low compression, moderate boost from a slow turning blower then a truckload of boost from a real big turbo that would otherwise be to laggy, but you do increase cost and weight and complexity.
In a boat, you have the option of a really efficient inter cooler due to the infinite supply of cold water.
Rod to stroke does not have any significant impact so long as it is not out to lunch. The difference between 1.7 or 1.8:1 will not matter, but 1.4 to 1.5 certainly will matter.
A good oil system that cools the oil well and controls surge and windage is critical. Oil squirters to cool pistons certainly helps high compression, high boost motors so long as you can keep the oil cool.
Except for a stable slow idle and somewhere to hang the ring gear, a high speed power boat does not need a flywheel. I use aluminium or a flex plate. The flex plates tend to bend from bendix drive engagement if the ring gear gets rusty, so that depends on amount of use, conditions of storage and maintenance.
For this sort of application, I would use a blower drive hub with inbuilt torsional vibration damper (most commonly called a harmonic balancer). It would be steel, a tight interference fit on the crank and have two 1/4" keys or one 5/16" key, carefully hand fitted to a gentle tap fit in the crank and the hub. It would also be as long as possible to maximise bearing area in the crank and hub.
I have seen marine grade intercoolers, but I can't remember where
Regards
Pat
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