The plans call for drilling the ribs, spar, and lower skins first. I did drill the ribs/spar and the aft end of the ribs to the lower skin (faux rear spar) (Edited – for some reason these are piloted #40 but need to be drilled #30. I missed this until it came time to rivet and had to re-drill them then). but then decided to assemble the upper skin, shims, and flap hinge and then drill everything. The shims that fit under the skin where they overlap were easily made from the supplied wing trim bundle. I clamped them to the rib on the underside and match drilled them with the rib holes. For the flap hinge, the drawing calls out a nominal 1/4" edge margin for the line of rivets with a minimum of 3/16". To give me the maximum adjustment for when it comes time to attach the flap to the wing, I marked the hinge at 3/16" and then drew a line down the flange to guide clamping and drilling of the hinge.
