Good news on the leak.
1. Be very careful of epoxy coating. It is almost completely waterproof itself, which means it will just as effectively seal water in as out. I think you mean where the sloping rear filler piece of the case (between the two ply faces) meets the hog. I reckon a winter job – dry it out thoroughly and cut and epoxy a small mahogany plug to fit the gap.
2. Shock horror – wood filler? Not on your nelly. Get a plug cutter and some similar coloured mahogany, drill the screwhole out and glue in a wooden plug. Carefullt alligning the grain of course. Thicken the epoxy with some microballoons that are brown or even better some mahogany dust.
The blackening will always be there I am afraid. It will fade a bit when thoroughly dried, but not disappear. Another tip – when screwing anything to timber, remove the screws once fitted, drip varnish into the hole and then refit the screw. Then no more black bits.