RE: alignment of wing, fuselage and tail surfaces?
Comparing two different measurments one referencing the nose and the other the tail will likely be off no mater what even sometimes with a new airplane much less one that has has had major fuselage repairs where an intangeble bow has been built in.
I do a lot of rebuilding primarily from dumpsters and some of my own simply because its fun and everyone a different challange. I have found with one exception The very best measurement is done with my eyeballs not a ruler. For planform alignment stand the airplane on its nose with the wing installed with the wheels aginst a garage door or wall and step back twenty feet and look. Any misalignment will be obvious and for side to side alignment just set the airplane on a table the same height as your eyeballs and step back agine 20 feet in front and look. Any needed adjustment will be obvious. For what its worth on this adjustment its best to keep the relationship (of the wing and stabilizer) the same even if it is a little out to the fuselage. Then its easy to set the vertical ninety degrees to the horizontal.
What often happens with a box section fuselage is the fuse bottom does not end up quite square in rebuilts and it won't set quite square on the table without the gear when aligning the wing and horizontal.
John