I received the new hinge material from AC Spruce. It took 2 hours for me to align everything, and the get the courage to drill the hinge material.
First I aligned the aileron with the angle previously used to rig the aileron pushrod. That way I could align the flap with the aileron in the neutral position.
I used a long angle and taped it to the flap. I could then move the flap/hinge up and down until the angle layed flat on the trailing edge of the aileron.
I had to make sure I put some clecos through the skin and the flap bracket, to make sure they were aligned before drilling holes. There are no holes in the hinge for the clecos to go through, so I spaced them out enough not to warp the hinge too much.
Drilled holes at the ends, then carefully drilled into the hinge every several holes.