Phil,
Flap position relative the fuselage bottom is not a credible measurement of wing incidence.
If you measured wing incidence as per instructions and it was ok before drilling, it is ok.
My flaps do not fare with the fuselage bottom equally after alignment with ailerons. This bothered me so I called Vans, it is as it is on some airplanes. I thought it would affect lateral control in flight but I can not detect anything unusual. The airplane fly's well.
Your wing incidence will be ok, press on.
