I have removed the outboard well flaps from the other side now. I used the Bosch multi-tool with a scraper to loosen it, which made it much easier than just working a screwdriver around the edge. I also found it is wonderful in removing hardened barnacles, which just fly off.
Crawling about underneath I used the multitool on the layers of sealant left on the underside of the hull, and again it was a revelation. where I had anticipated a horrible upside down job with a scraper and a face full of filth, the sealant just rolled off. It looks as though the hull had been copper coated before the faring panels were fitted, so I haven't exposed great areas without anti fouling. These is still some left, but it should be fairly easily removable. What I have discovered, on putting the outboard back on board to check clearances, is that I can now turn it almost through 90 degrees each way. What had restricted it before was a flange on the engine leg hitting the edge of the plywood covering the flaps. With that plywood off, the engine can turn much more.
I have made up a dummy faring panel, which I have sawn in two, length ways. It seems to have room to be hinged open, but I am going to have to fit some temporary hinges to check that it really fits. If it does I shall get some proper marine ply and do a proper infill job. Not what I planned, but I think it could be better than the original flaps.
I can't over emphasise just how useful I have found the multi-tool. I thought it was a bit of indulgency when I bought it, but I use it for everything. It is better than a hack saw for delicate cutting and better than every other sander I have got. Cleaning off half the sealant layer used up one battery, but by the time I had used a second one to clean off the other side, the first battery was recharged. I love it. I have also bought a drill and impact screw driver from Bosch, which use the same batteries, so I have four batteries and two chargers. Having separate drill and driver again speeds things up exponentially.