Hi Brian...I got your PM.
As I mentioned in my short message, I have some doubts about adapting the design in this way. I think you might end up with something better if you design an entirely new double-ender (or, as some have suggested, adapt a design that's already a bit closer to what you have in mind).
Blackfly was an experiment with a fairly narrow design brief. The object was to make a quick and manoeuvrable sailboat could be portaged by one person and carry as much as a sixteen foot open canoe. To accomplish that, I put a lot of volume into the hull (hence the boxy midsection). Also, since I planned to sail it often, and row it only when absolutely necessary, I gave it a lot of rocker and a bit of a flat run. Below the waterline, it's a bit like a Sunfish, in some ways.
If you keep the 4' beam and those fat middle sections while removing the transom and shortening by two feet you end up with a very different sort of boat...a very pudgy, buoyant little thing!

Having gone that far, I don't see much reason not to redesign the central and bow sections, too...maybe soften the bilge a bit. Of course, the sail plan will need to be reworked anyway, and you'll want to recalculate the location of mast step and daggerboard. You'd be wise to redraw the sheer. In the end, it's hard to see what you gain by starting with Blackfly.
I think a lightweight lap-ply cartoppable peapod is very good idea, by the way. If I were to do Blackfly again, I'd probably do something very similar to what you're suggesting. However, I think I'd start from scratch, rather than try to modify the old plans...