I"m not a fan of riding a bike at Embarcadero. I would like to see more bike/walk areas like the one on Townsend between 7th and 5th where there is a clearly marked bike only and walking only section.
The last time I rode my bike to the Caltrain, which was admittedly a while ago, everything was being ripped up on 5th near Townsend (I think it was 5th at least -- it was one of the nearby numbered streets); is that all finished now?