I've finally gotten everything dialed in, and today I rode 81 miles with no discomfort. I'm going to micro-measure everything on the bike. The biggest factor may have been the bike shorts. Today I wore Aerotechdesigns Classic Padded shorts. These may be a little better than my recently purchased Aerotech bib shorts.
I also wore a lot of Queen Helene's Cocoa Butter Creme on my butt.
Seat is even with the handlebars and saddle angle is totally level.