They could have done an AIrside AirTrain. Each stop the passengers goes downstairs to a tunnel Post Security with Security Clearance happening at a Central Security and Checkin Center could be somewhere off McDonald Rd where people clear Immigratio and Customs here via a special Shuttle Train / Retrieve Luggage etc. All cars are directed to this central processing area at staggard times. The road could lead from a SFO Shopping Mall a with Restaurants etc located off Anza Blvd where people can also be dropped off here and walk in an enclosed moving walkway to the central processing area . Rental Cars would have their Center in the Mc Donald Garage. Parking would be at various Garages in Center Terminal with a seperate checkin and Security Operations with a Bridge to Airside.
Other option would have been to just connect all terminals airside at time of rebuilding.