If you are looking for a shop that defacto specializes in audio stuff, I know of Neal Fey (company name) in the Santa Barbara area. They have always done most of the high-end audiophile enclosures. I don't have a number for them though. There is also Burbank Sheetmetal who does OEM enclosures for various companies ( they are also behind the Rackman series of products).
But there is no need to limit yourself to a shop that does audio-specific products. Up in your area (Bay Area, right?), you should be able to find plenty of good, well-equipped shops. The trick is finding one that you can establish a rapport with. Believe me, it's a whole new world when you start engineering your own enclosures, and you'll need to find someone who is willing to spend a little extra effort on your behalf. Bring a drawing around and see what reactions you get.
As far as waterjet versus CNC, waterjet is great for through-hole stuff but it does have its limitations as far as how closely you can layout your controls (i.e. cut out density). If your panel is "two-dimensional" it is the cheapest way to go.
Then you need to go on the painting and powdercoating silkscreening, anodizing...
