Had a custom 6 built a few years back. Just be absolutely certain you a) want/need a 6 string and that the specs are exactly what you want now AND, as far as you can tell, will suit you in the future.
I'm a flighty git. I got exactly what I asked for, but by the time it arrived my tastes had somewhat changed (took almost a year from start to finish).
My advice would be to buy off the peg if at all possible, even if you can't get exactly what you're after you'll get close enough that a few modifications will get you all the way there. Live with that for a while to make absolutely sure a custom is what you're after. Think of it as an intermediate learning step.