Don't worry, we've all had problems somewhere in the nether regions.
1) Are you using really good shorts with a chamois meant for long distance riding? I like PI's PRT chamois and flat stitched seams.
2) I changed saddles which helped
3) Chamois Butt'r -- I swear by the stuff for long distance rides or when I'm riding several days a week. It comes in large tubes as well as pocket size packets.