The former WP caboose in Oakland that mentioned along th waterfront is actually former Tidewater Southern, I remember seeing the sign board and verified it when it arrived.The shot of the rail next to Bart in East Oakland is a location once known as Clinton where the IER crossed the WP at grade. There used to be a tower when the IER weas there. The yard is former SP and still is used.
The track you show crossing Ashby Ave, in Berkeley is the former SP 9th St spur that originated at Shellmound. It once was the double track IER commuter line abandoned in 1941.
I can update the info on any of the many other photos you have displayed in your website.
The former Western Pacific main line that ran down Third Street in Oakland saw its last train in November 1996. Source: The Railroad Press magazine, issue #92, pp 36-37.