There should be a small hole in the aileron bellcranks and mounting brackets. When I adjusted my -4 ailerons I put pins in the holes to properly locate the bellcranks. I then adjusted the pushrods to the stick to center the stick.
I had adjusted my flaps to the proper full up position, and so then I adjusted the ailerons to be in line with the flaps.
What I found was that the ailerons did not line up with the wing tips, so the wing tips were not installed properly. No way to easily fix that so I just left it the way it was.
One think to check if trying to align ailerons and flaps is that they are not bowed, warped, or twisted. The right flap on my -6 warps up about 1/8" in the outboard third of the flap, so it is impossible to get it all to line up perfectly.
YMMV