in terms of workmanship i don't think there is too much variance... depends on the guys who you'd like to deal with and can trust your precious instrument with.
i've had setup and a nut replacement done by KC at zen. these days zen is really busy/popular and the lead time can get long. beez from look for beez is another guy who i'd go to, also considering that his shop location is convenient for me. never had any 'major' work done by him, but he's a great guy