If it's something that has just developed - could it be your shorts? As in are you wearing shorts that weren't designed for such long hours in the saddle?? I wore Bellweathers from March to about Aug when I started getting saddle sores!!

something I had NEVER had and I wore those things for my first 1/2, my first metric and 3 of my centuries. The padding in the shorts had just worn thin coz they were cheaper shorts and weren't designed for that kind of riding. I've switched over to Performance Century Shorts and the saddle sores are all gone!
Just my .02