I know the San Francisco Bay was fortified against Confederate naval units, but did anything ever happen there - or for that matter, anywhere else along the California/Oregon/Washington coast?
There sure was! The most notable action in the Pacific during the American Civil War had to do with the actions of a Confederate raider CSS Shenandoah. The Shenandoah was outfitted in England and was actually a hybrid type vessel, in that it could power itself by either its steam engine, or its sails. It is notable for being the only Confederate vessel that actually circumnavigated the globe, as it started in England, dipped down around South Africa, refitted and supplied in Australia, then went all the way up to Alaska in the Bering Sea to plunder Union vessels (mostly whalers). In the grand scheme of things, it didn't have much of an impact on the war, yet it was wildly successful in its mission, as it sunk or captured something like three dozen Union vessels.
The interesting thing about the Shenandoah is that it took so long to get to its intended region (Bering Sea) that by the time it really started causing trouble, the war had ended! This meant that the captain and crew were technically pirates rather than enemy combatants, so instead of getting paroled and sent home if they got caught or surrendered, they could have very well been hanged. They knew this, too, so when they learned that the war was indeed over (and that a fleet of ships was on its way after them), they took the long route to England so as to avoid any encounters with Union vessels. They cut south, down the western side of South America, then rounded Cape Horn, and made for England, hoping that a neutral port would provide them some level of protection. Their story is a really interesting one, and worth reading up on! I'd recommend 'Sea of Gray' by Tom Chaffin - it is a really easy read.