I'd go to Shelter Island Boatyard for the bottom job. See Bill Roberts. For the rest, it depends on the extent of the work you plan on doing. For very expensive, but nice work, go to Driscoll's or Knight and Carver. For run of the mill work, Shelter Island Boatyard, South Bay Boatyard, Driscolls other yard (Kettenburg) and Kohler Kraft are fine. Kohler Kraft specializes in wooden boats. South Bay has a good reputation for LP jobs, as does Baja Naval. The thing about Baja Naval, is that they're in Ensenada, (Mexico) and you need to BE THERE THE WHOLE TIME, but the price is right. Stay away from Nielsen Beaumont, they're a ripoff.
btw I've been using Bill Roberts's yard for more years than I can remember, and I worked in the Kettenburg yard as a teenager.
50 years boating in San Diego,
David