Don't fill the voids between the frame bays with foam, you'll just create a boat that will rot quickly and this is the worst location for floatation in a boat. You want the floatation high up, under decks and along the hull sides, not below the sole. I would also recommend using slates or a grating, instead of plywood for this sole, so things can drain below, then aft to a transom plug. Simply put, water will get into the boat underway, it's the nature of the beast, so provide a place for it to accumulate and can be pumped or drained off, when you're done for the day.
As far as her looks as a "work boat", this shape isn't typical for a common working skiff. The bow rake is extreme and the entry a little too fine for this look to be really accurate, but it doesn't really matter, as you like the look. She's more a pleasure boat version of a skiff to me. I think she's a bit dainty forward and initial reports of trim problems with the first builders suggest this is the case. This will be more so with a modern 4 stroke hanging on her butt. To me the shape is better suited for blasting along at high speed (relatively) then actually working the flats, poling around in the saw grass and especially casting from the forward section of the boat. This is where the more typical shapes come to play. They're fuller forward to offer enough volume to make a stable platform for a casting deck or generally "working" from that end of the boat.
This would be a typical bow profile and sheer of a working skiff. The more vertical bow permits more volume forward to support someone working fenders, lines, fishing, pulling a trap, etc. There's enough rocker forward to get the bow "free" in plane mode, yet enough immersion so she'll offer "bearing" if you're forward in the boat. As far as sheer shapes, well this is pretty subjective. I like Digger's, but it's nothing special, simply a blatant knockoff of working skiffs, where the forward sweep and flare helps keep the boat dry, without hindering forward vision underway.
I say screw the Acad model and just start tossing frames together. You'll find the inconsistencies when you spring the chine battens and a cedar shim or two will fix this a whole lot faster then mousing around on a computer. If you do develop a Cad model, publish the developed panel layouts, as I'm sure this would simply a number looking to build a taped seam version of this boat.