I've been using Addict Surfboards for the past 3 years and you can't beat the price, Micah is a super shaper, he's located in Sorrento Valley. I work in National City, but to me it's worth the drive. A fiberglass board up to 7ft will set you back $385, paint extra but if not complicated he will do it for as little as $25 . Here is a link to some of his boards, but call the phone number, Micah doesn't checks his email all the time:
http://www.surfingsd.com/ad_spots/board ... rdroom.htmCloser to Chula Vista, TNT surfboards has a bunch of shapers at their bays, they are in Imperial Beach. One I have used and dig is Novak Surfboards, Jay Novak is a great shaper. A fiberglass board is probably $460, paint another $40+. Here is his link, but once again, forget emailing him:
http://www.tntsurf.com/Lastly, if you want some in San Diego, and want to go higher end, google Plus1 surfboards and Sharpeye surfboards, both do customs starting at $495 + paint. Great brands, but you are paying the difference. Call them, they don't reply to emails either. Both located in the sports arena area
Honestly, of the three, I keep going back to Micah because of the price and because he keeps getting the boards right.