I've had some knee and IT band problems in the past, but it was always my left knee/leg that had problems and some pain. It wasn't intense pain and it was usually better after a day or two. The right knee and leg was always fine. So the bike setup seemed to be fine for my right leg, but not for the left. This would tend to indicate that the left leg had some kind of problem, like a difference in length.
However, my leg length seems to be pretty close, or at least not different enough to cause the problem I was experiencing. The problem is, I'm flat footed on my left, so I tend to have an internal pronation (my leg drift laterally inward slightly at the foot/ankle on the down stroke and straightens out on the up-stroke).
To correct the problem I tried shoes with more arch support, but even that wasn't enough. The next step for me was to try using a Bike Fit system called "The Wedge". It comes with a package of plastic wedges of varying thickness. The procedure for installing them is mostly trial and error, but I wanted to see if I could apply some methodology and documentation to test the results of trying different wedges. For the problem that I'm experiencing the thicker side of the wedge is installed toward the big toe side of the show (left side in the picture below) which raises the instep of that shoe.
Here's a "Wedge" from the kit installed
on my left shoe between the cleat and the shoe.