Legs-KEEP THEM WARM. Your knees have very little insulation and when it gets cold, the fluid in your joints does not have the same viscosity as when they're warm and you risk ruining your knees in the long run. I wear Defeet Wool Kneekers which will stay warm even if wet. Any wool knee or leg warmers will do. If it's really cold, You can go with tights over your shorts but it doesn't generally get that cold in the bay area.

Feet-I like dry feet more than warm feet but they usually go hand in hand. I have a set of Bellwether Aqua-No booties for when it's wet. Other times, I just use wool defeet socks.

Chest-A standard base layer and my jersey is usually fine for me. If it's a little colder, I'll throw in a wind vest. If it's wet, I'll use a light rain jacket, but remember, you'll end up sweating under that jacket and be wet anyways.

Arms- Arm warmers are usually fine for me. I alternate between Defeet Wool Arm skins or the arm warmers from Voler that match my team kit.

hands- I have a set of full finger mtb gloves that I use on occasion but usually I just go with half gloves (because I forget to grab the other kind). I also have a pair of thin wind proof REI gloves that I will wear over my half gloves for extra warmth.

Head- I generally don't have an issue with keeping my head warm but when I need to, I wear a thin coolmax skull cap under my helmet that can also cover my ears. Remember, dry=warm.