Well, decided after a bit of trimming and fitting that the motor well sides that I had cut will be ok. Not perfect perhaps, but I think they will work out fine. If the slight misalignment my bad cut causes problems later, it will be at the joint with the deck and I know how to fix it easily there. That will save me 1/4 of a sheet of MDO, at least.
A nights sleep and a fresh look let me solve the “bracing problem” quickly with a board below the transom pieces and a short extension up to hold each in place side to side. Worked a champ and just took a few minutes to put in place. Why that method hadn’t been obvious to me yesterday, I don’t know.
As promised, here’s a picture of a “chine stretcher”. You can see (around all that messy epoxy work) a small plug and a backer plate/board. Seems quite solid.