Aileron alignment shouldn't be too much of a biggie to establish. Earlier kits required the builder the fabricate a large contour board which was a full size outline of a wing cross section. It was drawn with a magic marker on the bottom of the shipping crate. It had to be cut out and fashioned into a workable part. A cumbersome process, the newer tooling hole trick is a much easier technique to work with. Still, I'm not sure that establishing the absolute precise center of your now rounded out tooling hole is really going to be all that critical. In the end, you want the trailing edge of the wingtip, aileron, and flap to be in alignment with one another when the aileron is in the neutral position and the flap is up. There are any number of ways to approach the task. For instance, here's something I did. Not easily seen in the photos, there is a string taped to the floor and 3 plumb bobs are draped over the trailing edges and in contact with it thus assuring overall "straightness."
I don't know if the pushrod lengths on the plans have changed or not since when I did mine. I found that I needed to adjust the pushrod lengths a bit to get the aileron neutral position and travel correct.
