There is a Building a Home forum that might be helpful.

Building a Home

Of course you should ask the folks in the building forum. Here is everything I know from living in SF (peninsula.) Hire a very reputable contractor with deep knowledge of your town's codes and architectural review process. Where I live permitting is a nightmare- from whether or not your roof line blends well enough with your neighbors' to how your dishwasher is installed can all be tricky. You need people who know what to expect and have the relationships to help navigate the process. Congratulations on the new house!