Coming along nicely! It would appear to me you must have extensive background working with wood.
Your mention of limber holes probably warrants additional discussion on two fronts. One is the necessity to seal the holes. Some simply coat them with epoxy. Some will fit a piece of epoxy tape to the surface. Others will go so far as to epoxy in a short section of 1" outside diameter PVC pipe, flush on both sides or protruding slightly. That would pretty much seal it up.
Second part is the tradeoff of having each compartment drain to a central bilge to be pumped out, vs. knowing that if the boat were ever holed, water could then back through all those limber holes and flood the boat, potentially allowing her to sink. Without the holes, water will be contained in the damaged area, but would then be trapped in those compartments, which over time, would be equally bad.
On balance, my guess is adding the holes is best as water from a variety of sources (including condensation) may get in and needs to get out. Punching a hole in the boat is pretty rare. One option may be the use of a few one way check valves at key points in the system. Those are pretty simple to do.