Are your shorts at all baggy? A really form fitting chamois will help prevent a lot of chafing. I raced this year in a borrowed skinsuit (my BF's) some of the time, and even though that would be for really short races, it would get pretty uncomfortable just because it was 1 size up from being a really tight skinsuit. The chamois would move around a little too much.

You might also want to tinker with the angle of your saddle to be sure you're putting pressure on the right spots and avoiding pressure elsewhere. That won't really change your bike fit. Just tilt the nose. The angle of the saddle that's the most comfortable for you may vary between saddle models too. For example, with my Jett, I had it nose down a fair bit. With the new Ruby, the way it broke in (really sunk in where I sit), I need to point the nose up so that when I get on it and it sags in a bit, I don't wind up shifting my weight too far forward.