I had EXACTLY the same symptoms as you, in my 'come back to Audax' year (1993). The pain started 90 miles into my first ride of the Elenith and just got worse. I finished though.
Took it easy on the bike for a few months, but when I started training for long distances, the pain returned.
Went to my doctor, who sent me for an X-ray to see if I had the beginnings of arthritis in my knee. Results were all clear. My doctors response was, 'you'll just have to live with the pain then'
I bought a book called, Knee Health...Problems,Prevention and Cures by Vivian Grisogono which was quite informative and made several constructive suggestions on how to sort out my knee problem.Of particular use was the suggestion to raise my saddle.
Somebody at work suggested a sports physio who might be able to help me further. When I consulted him, he said that I had Iliobial Tibial Tract Syndrome and could sort it out in a few sessions.
He manipulated the knee,applied heat,taught me some stretches to lengthen the ligament and after 5 sessions I was cured
I still have the knee problem book and can send it to you if you wish.