I went to see the Physical Therapist today. He listened to my history and based on what I described and what he saw by examining my feet and knees he recommended Orthotics. He said that I could be running in shoes that had more motion control / support but said that Orthotics were really the answer. My arches are pretty flat apparently and this is causing my knees to turn inward, putting more pressure on my ankles, tibia, and knees.
He didn't agree with the Sacroiliac theory, which will be interesting to talk about with my cousin who is also a PT. (I bet she's heard of him) He measured me for Orthotics by taking a cast of my foot with some sort of plaster soaked fabric that he'll send off to Brea, CA where they'll be made according to the molds and the notes that he took as he examined my feet. He recommended against the Carbon Fiber orthotics, saying that they were too rigid for me. Mine will be some type of ABS plastic. I'll see them in 3 1/2 weeks or so. He recommended that I don't run until I get them.
He was surprised at the lack of flexibility in my hamstrings even though I told him how horribly inflexible I am. He gave me two exercises to do for my hamstrings and set up a couple more appointments for me.
I hope my health care covers some portion of the Orthotics, they're expensive!