I think that is the best question in building guitars and one that has no real answer that I have found, only preferences really. Some of the order is set in stone, but much of it depends on many different things and what one prefers and what is possible with the tools you have. I spent more time planning the order of the steps, I swear and I ended up having to change things as I went when I realized that I couldn't do this with the top on or I had to do the binding before this, but after that and so on, lol.
How did you mark out the pup routes and neck route and bridge posts, it seems they are all apart of the same center line your neck should be on, should be fairly easy to line up. The way to keep it easy and precise is templates and center lines. Your best bet for the bridge and stop will be a drill press. Best of luck. J
well i did go off the centerline for everything, but when i fit the neck, it must have been off 1?16" or so...so it threw the PUP cavity off.