Here's some progress from earlier in the week. Fuel tanks came out exactly as I designed them and are sweetly fabricated - all 3/16" 5052 aluminum. Total nominal volume ~ 132 gallons. Should get an honest 110 gallons of usable volume - hoping for 3.5mpg resulting in a range of over 350 miles so I can go a week to 10 days on longer remote trips and screw around a lot without worrying too much about fuel.
Raised the back deck 3" higher than the main cabin floor, giving just enough room to run the fuel lines above the main stringers and have them completely outside the cabin - zero potential for fumes in the cabin other than the wind wafting vent fumes into a window occasionally perhaps. This, too, came out exactly as I designed it - super happy with the whole works.
Cuddy is mostly built - aft cuddy bulkhead is at 118" - the longest length recommended by Brian. The cabin will be 9 1/2' long (about a foot longer than Brian recommends), still leaving 8'-3" of back deck from transom to aft cabin bulkhead, which will be cut down by about 2-ft for the splashwell and maybe 16" or so for the cabinets on either side of the splashwell. Since I'm focused on camping rather than a total fishing machine, these compromises seem reasonable. We pushed the height of the cuddy up a few inches so I have 40" from bunk top plywood to cuddy roof, so I can sit up straight in there. We also eliminated stringers in the cuddy roof - we have 1/2" of foam glassed both sides, with 1/4" okoume laminated on top. With the hatch flange, the windshields, and a curvature of about 4" in 6-ft, it will be solid. It already feels fine without the windshields and hatch framework in place.
Decided to have zero access ports in the back deck floor - just seal it up tight, no hatches to leak and fuss with. The floor of the cabin and cuddy will have removable cutouts to access storage there.
In the anchor well, we moved the bulkhead up to 48" instead of Brian's 51", to give the hatch a bit more room to swing without hitting the windshield, and create a hair more space in the cuddy. Still seems fine up in the anchor well so seems like a reasonable tweak.
Finally, getting back to Brian's concern about the transom, we measured that and it checks out perfectly - cutout is 18" below the gunwales, and height from keel to cutout is 25", exactly as our engine vendor specified, so we're all good there.
Open to ideas on what to coat the back deck, gunwales, anchor locker, and cuddy roof with. I originally wanted bedliner, but the bedliner I've seen has too many "holes" in it to trap dirt. Curious about Zolatone or other products that create a grippy texture that is still reasonable to clean.