I trial fit the neck of the ES-1 to the body back when I first got the kit. It was straight to the body but always had a bit of a wobble that would change the bridge height.
Finally sat down to decide how I would shim the pocket on Glueing Day. Turns out the shoulder of the neck would pivot on the face of the body. I could set the heel of the tennon into the floor of the groove, or I could rotate the neck back a couple degrees to sit flush to the toe of the groove and seat well around the side wall.
Back and forth, pros and cons. The bridge and action sat better when the heel was shimmed so I dry fit enough splintered veneer to pivot that way. Also shaved the fulcrum off the shoulder of the neck to sit all the way down into the groove. AND had some more veneer ready to shim the sides of the groove that weren't perpendicular to the floor of the groove.
So a lot of fine tuning and dry fits! But once you rehearse it enough - even down to what order to cinch up the C-clamps - when I realized I can't get back to to build for a couple days... Well, I hadn't planned on setting the neck today but *shrug, here we go!
Lay in the glue, set the shims, hand fit the neck one last time, check the wobble is gone, fit the first clamp and veneer covers for the jaws, arrange the second clamp, reset the first clamp, check the angle is right, then stuff veneer and more glue into the remaining crevices [panic just a little that I'm sure I put enough glue in there?], and then gently, gently set it back down to cure. And check the mating surfaces are mating as I expect, again. [And I'm going to check again after this post!]