Neck alignment on a scratch body build is a tricky thing to get right! It is definitely a situation where you need to measure more than twice (in as many different ways as you can think of), and route once.
I used the 2 strings approach (both outer and inner ways mentioned by fender3x) with the bridge in position, draw the neck foot on the body, then line up my routing template. This was most nerve racking on the jarrah striped bass as I needed the strings and bridge aligned with the strips!
https://www.buildyourownguitar.com.a...l=1#post226952.