Are there any overnight / long term parking lots near here? I have to commute from Manteca to the east side of the bay near Pali Alto. Rather than commute to San Jose via Ace then get CalTrain up to Palo Alto I’d rather cross the bridge by car.

Yeah. It's fine. Leave your car unlocked with nothing in it, that way they don't break your windows. Sometimes they'll smoke crack or shoot up inside your car and leave paraphernalia behind. Make sure you check before you drive across the bridge. The police won't believe it's not yours.

There is the ACE train parking lot. You can park overnight, but it is not secure.