Hi Jbees, best do a mock build, clamp the neck in place, put the pickguard and bridge in place, install both E tuners and put the low and high E string on. Clamp the neck so its hard up against the bass string side. Move the bridge around to make sure you can get a fairly equal offset of both E strings to the edge of the fingerboard. If you can do that, I then remove the hardware and drill the neck screws in, making sure the neck heel is flush in the pocket and butt up against the edge of the bass side of the pocket. Does that make sense ?
You can drill the bridge in place once you do this process again and the neck will be screwed in place this time.
A more solid neck to body join will give you more sustain and should keep in tune better.