After locking both ailerons in the zero position using the aileron jig fixture, I clamped both flaps to the ailerons, 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 left flap gap is about 1/8" and the right flap gap is about 1/2".
I'm not sure exactly what I'll end up doing, if anything, to address this. More research is needed.