Gilly,
The best thing you could do for your 45 flintlock, is a complete make over. You need to put that fat girl on a diet. The original maker left way too much wood on it pretty much all around. the lock panels need thinned down, and the architecture over all needs to be refined and thinned. Clean up the muzzle cap area. It is too bad that he put the front sight so far forward on the barrel, it makes everything look stubby. By the time you get done rasping and sanding you will not have any finish or stain to worry about. Study and handle some originals or if unavailable some good color photos of well made guns, then see what needs to be done. I know this may seem harsh, but you will end up with something that you can take ownership of. This is the first lesson of gun building, correcting mistakes, yours or someone other person's. Best of luck go slow and enjoy the ride.
Ron