primarily with a heavily dammaged fiberglass canoe that was quite floppy without its rotted gunwales but was still stiff enough to be worked on without the rails. I suspect your boat with wood ribs will not be excessively flexible without the rails. I would take them off first.
I put structural quality of the patches first and cosmetics second since I dont believe in fully hiding the repairs. I think future buyers should be able to detect some cloth texture at the patch to see that the patch was made with cloth and well squeegied out.
I cant help you with the ribs. I have no experience there. good luck
2-3 Canoe/Kayak Trailer
Wall Mount Boat Racks