After locking both ailerons in the zero position using the aileron jig fixture, I clamped both flaps to the ailierons, and finished trimming the flap skin to match the fuselage skin. After doing this, I discovered what many people have found before me -- my flaps don't line up flush with the bottom of the fuselage. Specifically, the right flap hangs down quite a bit further than the left one.
I'm not sure exactly what I'll end up doing, if anything, to address this. More research is needed.