I drilled and clecoed the flap hinge to the right wing tonight. Turned out pretty much perfect, at least as far as I can tell right now.

The inboard end of the flap (bottom left part of picture) is sticking out because the fuselage is tapered where the wing mounts. It gets narrower the further you go aft. The space between the wing and fuselage is of variable width, but it is covered by a fairing, so you never see it. The flap doesn't get covered by the fairing, so it has to be longer to come right up against the side of the fuselage.