I have an old Robart incidence meter, works decent for setting the thrust line.
I generally,
1) Mount the motor,
2) check the thrust line to wing incidence, adjust as needed
3) set the horizontal tail to the wing
4) check the tail to the thrust line as a check
5) use a string to check the centerlines - I switched to SpiderWire because it has no stretch and I had some.
But I still rely on my eyeballs and design my fuselages with the stab, motor mounts and wing related to a machined edge ( the top ). Put a hollowed to .125" carved block top on and you should be good.
I'd bet the majority of guys build that way.