Great advice Bizman and Mister and great tips about the pilot hole method as the starting point for the long drill journey. I've come up with a strategy of routing a channel in each edge of the body (join edges) before joining (set neck, 2 piece body build). I will then drill the required holes from the channel BEFORE glueing the body up. Control Cavity covers for the main CC and toggle switch. This will take some accurate measurements and will still require some long drilling but I think I'll have a better chance of getting it spot on with this approach. It's also an insurance policy - if I screw up the long drill I won't have too much invested! I'll certainly read up on a few PG threads for some more tips.
Again, thanks!!!