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One advantage I have,is that the boat will only see freshwater (the Great Lakes)
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That may not be an advantage. Wood rots quicker in freshwater than in salt water. I've know old timers with wood boats that put rock salt in the bilge to make sure that any rainwater that got into the bilge became salty!
As for bedding the scupper tubes, 4200 or Sikaflex might be a good compromise. Life Caulk is pretty good stuff and will even cure underwater, but I still ended up with quite a bit of rot in the wood blocks and a significant leak after about 25 years. They also make stuff now that will attack 5200, but might be a challenge to get it in around the scupper tubes!