Have there been any allergies (plants, trees, etc.) identified as occurring between early october and early november in the san francisco bay area?

Grass. Fall weed pollenation typically concludes by the end of sept however, late rains can result in a second wave of grass pollenation. Rains and warm weather can also result in high mold in the air. Go to pollen.Com for local pollen counts in your area.
Weeds. Weeds tend to be a fall allergen....So weeds could also be the problem. Grasses and weeds are similar but different and definitely pollinate at different times.