Haven't done a set neck LP yet but reckon the neck PUP surround will cover things up and to check alignment you may need to loosely fit the high & low E tuners and run some string, cotton or fishing line down to where the bridge should sit as that will give you a better indication of how things are lining up.

If you are tempted to fit the bridge be careful not to drive the posts all the way in as they may not want to come out.