RV-6 flap/aileron alignment.
Randy,
Without having seen your project but after building several RV-3, 4 and 6's, I would suggest looking back to your aileron hinge mount vertical placement. Place the airfoil template over the wing to verify the aileron position.
The ailerons and flaps should both be inline with the upper and lower main wing skins. If the aileron is properly positioned, then move the flap brace (W-621) up or down on the rear spar so that the aileron, flap and their trailing edges aligned. Good luck!
Chuck Brietigam
RV-6XXL