Knee Pain

My knee hs become very sore again on the outside on the tibia, which I think is the lower end of the lateral collateral ligament. It's painful when I walk, or kneel. I suspect that its a symptom of changing saddle height (i'm trying to get a flat backed aero position for TTing) though the saddle is not *technically* too high. Anyone got any advice from experience etc? I think I may have made too big an adjustment too quickly maybe....
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Before making adjustments to the seat post height, place tape on the post:
a) touching the frame for raising the post.
b) a few mm above the frame for lowering the post.
This eliminates major errors when loosening the post
Notice you time trial. I've read that the aero time trialling position can contribute to a shortening /tightening of the ITB. Maybe some stretching and self-massage of the ITB band would help.
Using Speedplay zero pedals really helped my road biking as they provide good float. I can now usually cycle 50-70 miles on my road bike without any problems. It's the mountain biking thats giving me gip these days.
I've never really sorted mine and it is a bit of an ongoing battle, though it comes and goes.