I kept my 36' boat in Alameda for many years. Never had any serious problems with storms, even big ones, but...
1. Rain IS a problem if you have deck leaks, which most boats do. A deck leak may migrate some distance before appearing inside the boat, so finding the actual source can be hard. Worst case, seal the boat completely with duct tape, then turn on a blower inside the boat to create positive pressure, then use the common soapy water method to find the location of the leak from the outside.
2. No need to remove main, just wrap some more light line around the sail cover to make it real secure.
3. Most common problem in storms is the furling jib coming partially unfurled and tearing itself to pieces. Using another topmast halyard (main? spinnaker?) take many wraps around the outside of the furled sail and secure halyard well at bow. Or take the jib off completely.
4. Several years ago, one or two of the older marinas in Alameda had docks floating off the tops of the pilings during an extreme storm-caused high tide, then breaking off and taking 20-30 boats, still tied to their floats, all going for a mass sail up the estuary. Ugly. If your marina has older wood pilings, with some leaning in odd directions, I'd be a bit worried, but I think most of the marinas there are now in pretty good shape.
5. Even in non-stormy conditions, make sure all halyards are tied off away from the mast so the wind--even pretty light wind--does not turn your boat into the local "halyard symphony." Not good for the mast or halyards, and will absolutely enrage your neighbors.
6. Obviously, good docklines, maybe with those rubber snubbers to help with surge. If you are in a one-boat slip, two bow and 2 stern lines can center the boat in the slip so it has little change of rubbing. Spring lines too, of course, to prevent front-back movement. And lots of fenders, just in case. In a two-boat slip, doubled bow and stern lines, firm spring lines, and lots of fenders on BOTH sides of the boat (your slip-mate may not be as careful as you).
7. Keep the boat in the slip! Even in a bad winter, there are a surprising number of nice sailing days in winter. Some of my most pleasant sails, often in pretty light wind, were during February!
Enjoy!