Start out by charting what you would like to see ultimately. What are your values? Some good questions:
How long do you plan to live there?
Are schools important to you? Or is a good quality of the schools something you would like to have for future resale value?
How flexible or friendly is the city for the planning and building process?
What is the ground like? Is the parcel in a liquifaction zone (Willow Glen, parts of Alviso) where the ground is softer and foundations slip more readily? Is it in a flood or landslide zone?
What is the average price of a home sold and will my building and land costs exceed it (will I go in with equity)?
If you are only focused on commute, that simplifies things considerably.
Many builders choose to do a "one wall standing remodel" where they find a home that needs an overhaul and remodel away. This takes a chunk off of the price!
One of my favorite builders is Joseph Wetzel, "WetCon" construction.
Let me know if you would like more information about Joe or your home search.
Erica Glessing Nelson