A different saddle may make a difference for you.
As far as skin-soreness I have found a great solution, one I started using during my month-and-a-half as a full time bike messenger. I use vaseline "water resistant skin protectant lotion", which I believe is sold at pharmacies and kmart-type stores. (any lotion using more or less the same ingredients should work- the listed "active ingredient" is dimethicone.) I just put lots of the stuff in the spots where my skin gets chafed the most. OFten, pain that's not at the skin level will go down at least some if you make a conscious effort to relax muscles whenever they aren't really needed to keep you balanced and moving forward on the bike. For example, you have a lot of muscles that are there to control your leg's position but can't contribute to the forward-down-back-up motion of the foot- don't stiffen them up.