No Realtors are touching this question? I'm a little surprised. Ask 3 General Contractors and get 3 radically different answers. The shame is that you're supposed to know the loopholes and what questions to ask.
Keep in mind I'm a Journeyman Carpenter, who has built custom and tract homes, who became a Realtor later in life. My insight is multifaceted and volumes have been written on this topic.
First, get at least 3 estimates stating specifically what you want, from the foundation to the roof and everything in between. Will it include the utility hook-ups, driveway/sidewalk, landscaping/seed/or simple grading? Do you need an Architect or will they providing plans? Is the A/C and heating units green?. Solar? Warranties? Tile? Exactly what kind, where, quality, imported or domestic? Carpet, pad thickness, manufacturer, plain or cut pile, level loop, pattered loop... you're starting to get the idea.
Saving a buck is in most peoples minds and you may want to take care of installing floor ocverings yourself and that might save you a few bucks. Kitchens and baths are where the price/sq ft can be quite high and is where you can save if you're a do it yourselfer.
Most estimators in the bay area are throwing out numbers starting at $150/sq ft. Add tile in the kitchen and baths and that number goes up.
I can direct you towards a few Contractors who have built homes locally and whom I've done business with. Just let me know if you'd like those numbers. I am happy to help.