Between reading the comments here along with my head on pillow engineering session, My wife is used to my odd dreams now where I perform allot of my engineering, The raw water pump will definitely be used. It is the factory pump that needs to be questioned. Yes it is important in most all installations, especially a closed water system needed in salt. The closest this boat will get under my caretaking will be rivers close to the ocean, but they are a 6hr tow from me.
My thoughts now, raw water pump, probably crank mounted, might be belt driven. And probably no factory WP, although it reduces fabrication it is a redundant part for fresh water cooling. There are kits available for this task. Many of what I see are best in warmer climates than where I live, as such I will build mine utilizing a thermostat.
More later as I start building the powertrain.

good decision. i have a comprehensive parts list. i pulled my LS from a truck and built it from the block up. make sure you design this to be run at higher rpms.
think main bearings and connecting rod bearings (i used Kings XP or Clevite H would work), trunnion upgrade, AFM Delete, camshaft selection is key (torque over hp, and avoid reversion= max .224), head gaskets, head bolts, etc.

i'll warn you now the most expensive part was the exhaust manifold kit. make sure to do the math on whether you need a spacer on the riser. i needed one and had to custom fab those b/c they didn't exist on the ones i bought from hardin marine.

To kind of close this out, I expect my build will utilize a Jabsco crank driver pump. Took some time to determine which are China copy's and real Jabsco. The china pump has a screw between the ports and no stamping on the cover.
At this time I intend to do away with the factory WP, mostly due to it's use of a bypass style thermostat. No need for external flow. I will need flow for the transmission cooler, figure that out next year. Probably a pressure blow off valve feeding the transmission cooler.
The support industry offers allot of options for water manifolds on the front of the heads. Not sure if I will buy or build this part. I will revisit this next spring when I buy the engine.
The outlet will feed the wet headers, I will build my own. These will be 1.75 STL inner tube with aluminum outer tubes. I look forward to building these, should be sweet.
I want to thank everyone, well except one, for the guidance on this step of the project.