As to the type of pain, it usually started about 40 km or so into a ride, and became progressively worse. It was not a mild discomfort, it was real pain. It would extend from where this tendon attached to the bone below my knee, and continued upwards into my hamstrings. Walking would hurt afterwards, and I couldn't ride for a few days until the pain subsided, although it never went away.
Once, it became so bad during a ride that I had to ride back using my right leg only, and I couldn't walk for about 10 minutes once I got back to my car.
So how did I fix it? Well, after asking lots of people to no avail, I eventually figured it out myself (at least I think I did, so far this year I don't have the problem).
I first had my setup checked out by some knowledgeable folks to get the seat height and forward/backward positioning about right (I later made small adjustments). When this didn't fix my problem, I decided it was caused by the interaction of my cleats and my pedals. My setup forced my feet to be "straight" - by that I mean my toe points directly forward and heel points directly back. Trouble is, that's not how I'm built. I have lots of out-turn on my left foot, and forcing it to be "straight" placed it in an unnatural position. I assumed the repetitive motion of thousands of rotations in an unnatural position eventually resulted in damage.
To compensate, I first tried one of these things:
http://harriscyclery.net/site/itemdetails.cfm?ID=1331
I was looking to move my left foot further from the pedal, so my toe could point outwards without the heel hitting the crank (my cleats have lots of float). As it turned out, I didn't like this kneesaver thing because my foot was too far out. So instead I just moved my cleat to the right as much as I could, and I put a couple of washers between the pedal and the crank. Now when I pedal, my left foot isn't "straight" anymore, but angled in a way that is more consistent with natural positioning. So far so good, no pain anymore.
Hope this helps with your problem. Good Luck.