Good news here - you are looking carefully at the charging issues early in the design.
I think the next step as far as sizing is concerned is to run a few cost models on specific configurations.
If you decided on a 24 volt system, then you could use #1 wire, 100 or 110 amp fuse and have 1% voltage loss over 20' of wire at 40 amps. That would let you size a motor. If you don't like the answer, consider 48 volts. That lets you run smaller wire, or longer runs, and can deliver quite a bit more power on the boat for the same cost. For example, #4 wire, 20 feet, fused at 65 or 70 amps, and 1% voltage loss at 30 amps. So 150% the power delivered at less cost and weight. You just need to look at the options as far as motors and controllers go and see what fits. 24v X 40 Amps = 960 Watts. I think that should do for cruise, with the wiring supporting double that for an occasional sprint. Controllers will cost about $1 per peak amp, so not a huge expense for a boat.
Post three or four designs with batteries, motors, controllers, wiring sizes and lengths all speced and hang a weight and price tag each of them. And describe the actual charge and discharge cycles you envision for each design. It's really more about choosing from among options than design at this point. It would be better to run 60V from the panels onto the boat and have the charge controller next to the batteries than to have the charge controller near the panels and run 24 or 48 volts to the boat. They would be #4 wire @ 60V as well. So about $400 for wire and ends and fuses if you bought a 100ft spool of #4.