oops! we all do it, easy to miss the mark sometimes!
that brace piece has been on all the doors I've seen/have - I think it's likely there to prevent the opening from spreading and allowing the vent rubber to lose it's seal - should be on the front side of the vent post so it'll keep things tight, but shouldn't affect the big glass .... note that the track should be on the regulator arm rollers before the glass is attached to it, so the track holes can be lined up with the glass sash holes by using the regulator to raise or lower it ... and you need to make sure the extra arm is in it's short track on the door first, it's what keeps the regulator moving straight up/down
Bill