Gryphon Guitars in Palo Alto (Frank Ford's shop) has a tremendously capable staff - doesn't really matter which guy there does the work, there's excellent QC and oversight and a very deep bench.
Keith Holland's Guitar Hospital in Los Gatos is also a top-notch shop. They build their own line out of axes (well, two, actually, Los Gatos Guitars and Keith Holland Guitars, with the LG line being a lower trim line). Their builds often include Warmoth parts, and they are perfectly set up.
In San Francisco, Gary Brawer's shop inside of Real Guitars is the go-to for such luminaries as Joe Satriani, the Metallica boys, and so on. But he's often booked solid so don't go there with anything you need right away unless it's a real simple job. If you had them do a Warmoth build from components, it would be perfect, but you'd wait a while.
Also in SF, there's SF Guitarworks, who also do premium-grade builds. They've done a few builds for folks on this forum, in particular you should be able to find a "Swamp green" Strat by searching.
Sylvan Music in Santa Cruz does good work if you're on that side of the hills.
I know there are some guys in Marin but can't dredge up their names.
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