Xanthus, sorry I just read your thread I somehow totally missed it the first time I read through! In that last picture you can vaguely see the picup cavity routes. It goes RIGHT to the edge but it stays within the neck pocket mahogony.
About adjusting the neck, after I tested the bolt method the result was a perfectly fitting VERY tight and solid joint! So I decided to use NO glue at all and I'm happy with this choice, minus the neck laminates, which are running parallel throughout the neck minimizing any potential tone dampening, its all wood to wood contacts throughout the neck through the body!
I'm currently working on the tailpiece which will, again, be directly bolted, and mounted with wood connecting to the inner neck pocket that's running through the body of the guitar! The end result will hopefully be a very natural, open, fluidly vibrant tone!