I got the flaps down from the attic and installed them on the wings to see how they fit:
As expected, the inboard ends needed a little work to properly fit the fuselage. The flap skin was rubbing on the fuselage in places, and the gap was generally unsightly. The plans don't specify how much clearance you need here, but I've seen numbers anywhere from 1/16" to 1/8" mentioned. I decided to split the difference and shoot for a nice consistent 3/32" gap.
Instead of using a sharpie, I painted each flap skin with marking fluid and then scribed a line along the fuselage side with a 3/16" brad-point wood drill bit. Result, a perfect 3/32" line. (click for the big version to see it)
From there it was a simple matter of cutting and filing up to the line. After a couple iterations I was able to achieve a nice even gap that looks pretty good:
