I feel your pain (Really, I do). Same bike, same types of road surface for my 5 mile commute.

Are you posting over the potholes, or sitting? Posting helps greatly with the "pain" of the potholes. I've been kicking around getting new wheels, with more spokes, as I figure the more spokes might absorb some of the road a bit better too (Not really sure if it works that way or not).