Hi Scott
I was wondering why you say that the flap servo arm points toward the bottom of the wing skin? You say in your post that the manual shows it pointing toward the top of the wing. Did you get an update manual? I actually put my flap servos in the wing with the output gear toward the back edge of the wing and the arm pointing toward the top of the wing .I did have to shorten the arm on the servo and use the inboard hole. It actually worked out pretty well because the all thread linkage ended up being only about 2" long which should help it from bending during operation!!
Mel