After thinking I had solved this problem, I went on an 80 mile ride yesterday with excellent Aerotechdesigns bib shorts, and still had pain for the last 30 miles! Like you, the problem is mostly on one side, and I'm considering angling the seat slightly to one side (as recommended by Cobb).

Not for the faint-hearted, but after a ride in which you were sore, take a mirror and check out your butt. You may see red skin, which suggests that there is at least some surface component to the pain.

Too many variables:

Seat height relative to handlebars
Seat height relative to pedals
Seat fore/aft
Seat pitch
Shorts & Chamois
Butt cream present/absent
Saddle
Saddle yaw
Ride distance
How hard you ride
Positioning (spill the bowl or not)
Cleat position