Hi.
For a moment I thought you were my sister in law posting. She has exactly the same problem, which only started after we did a 100 mile ride when she was on her new Cannondale Super Six. She was assured it was not the bike, although we had done this distance many times before when she had a Giant. On advise she bought new shoes, Specialized somethings! as they have a built up bit inside which supports the foot. She has been fitted to her bike and is currently having physio, she is ok on short rides and Wednesday training but suffers over 50 miles.
I can imagine it is totally frustrating and wish you luck in resolving it. Have you tried another bike though just in case?

Dizzie