Parking the truck in San Francisco

We'll probably take him to the usual spots like the Wharf or Pier 39 and I'd appreciate any helpful suggestions.

Since you did not say much more than Pier 39, not sure what else you want to see but if it is the submarine and liberty ship you might well acquaint yourself with the bus schedule and routes to get you around. Once you park in SF, if you drive in and park, you likely will not be all that excited about moving the truck a mile or so every time you want to see something else. As to available parking at BART, I have never seen Concord Martinez full. Even for crew long bed duallys there has always been plenty of room. Some BART stations fill fast, on weekends it is usually much less busy.