When you do your aligning there, make sure that you have the wheel in place (or a dummy hub or a faux axle) tightened down securely to pull the stays / drop-outs into their "as ridden" position.

On my ST's dropout / DR hanger bracket area, I found it to be out a bunch. I used a machinist straight edge and then a couple of large (oppose pulling) Crescent wrenches to pull it around, not just in the vertical plane, but it needed a horizontal tweaking too! It's tricky sighting down a strait edge, but it can be done. It takes enough hands and some comparative (to the stays, chain rings and frame) measuring n' eyeballing to get r' done.