The first thing to know is that you can’t rely on the fret marker dots to be exactly centred. The book matching join on the veneer also may not be true centre.

Make sure there are no obstructions in the neck cavity. Clamp the neck on and see how it looks with the hardware in place as well. It also helps to run string from the nut to the bridge (do both e strings) as the will show the neck alignment from a playability sense.