Get rot is basically a real thin epoxy that will soak the wood and encapsulate it. I have seen way too much rot with wood under fiberglass to be crazy about doing it that way. Seal it up with a thin epoxy or spar varnish but keep it exposed so you can inspect it would be my thoughts on it. Just my .02 after having repaired many boat decks and stringers that are wood covered in glass.
If the wing lock back braces are properly installed they wont come off. I always tie the flaperons together as well as a just in case. I use castle nuts and a safety pin on the wing tie backs. Easy to put in and don't need tools but its secure. Every time I have seen the wings come unfolded when trailering was operator error by failing to secure them properly. if not secured properly they are going to do damage no matter which way its towed.
Not that big of an issue. Roll the gear box back and drop the mount down like you originally talked about. Its only metal and with a little time and thought you can make it do exactly what you want it to mr.
I am not sure how big of a hurry your in for the mount plate. I have the cad files done up for mount plates for the KF and was waiting till the CNC cutter shows up next month to cut them out. Making the engine mount holes 4" further forward is a snap with the cad..
The "stock" avid wheels are MATCOs. I had to put 2 spacers in each one wheel when I put the 30" airstreaks on them. You should be able to get away with one spacer in each wheel with the 26" tires. Call Matco, I am CERTAIN they have dealt with this a lot and can tell you exactly what you need to buy. Remember to get longer bolts to put the wheel halves together and longer axles as well.