New Construction
Each new instrument is built one-at-a-time in my shop. Wood comes from a variety of sources; Luthier supply companies will let you see high resolution photos of guitar sets on line before they are purchased, and I'm always looking for local sources as well.
I like mahogany for necks, with a quarter-sawn maple veneer sandwiched in the center for stability and strength, reinforced with two carbon fibre truss rods. I cut my necks to a pattern and finish them by hand with rasp, file, paper and scraper. 
An arched back is standard. The laminated tail block (photo below) is laid in extra wide for body stability and stiffness. Alternating the grain resists cracking in all but the most unfortunate dropping accident. To date all my new instruments have been maple, which to my ear has a nice bright tone with plenty of bark and growl.
I've used cones from Quarterman (can't get those any more, I'm afraid), Paul Beard and Tim Scheerhorn. Number 14 cast spiders, bone nuts and maple / ebony inserts are standard.
Waverley is my tuning machine of choice and all my plated hardware is the best available. Fretboards are ebony with wire frets. Inlay is whatever you can think up and can convince me to try. The Pearl logo on the tongue of the fretboard like the one shown above is standard.
Finish
The only sprayed finish I'm equipped to do at this time is water based. It's a non-flammable, non-toxic, thin, but very durable high-gloss finish. It produces a really good looking instrument without the danger of it killing me or blowing up my shop.
If you're interested in another type of finish, please contact me. I've tried lots of ways to finish wood over the years. I'll help you decide what'll work best on your instrument. Here's a shot of the spray booth.
Details
A fine custom instrument is a personal thing. I encourage lots of communication in the journey from conception to reality.