I have super-grumpy ITB's (and hip flexors, and hamstrings, and weak external hip rotators, and sloppy ankles, and pronated feet, and, and, and... typical wide-hipped-woman issues). That's why I haven't even considered trying clipless. It's not worth trashing the uneasy truce I have with my hips and knees and feet.
Ask your PT to do some myofascial release and active release techniques with you. She should also be able to teach you how to do your own MFR with your iliotibial band. Don't forget the ITB continues all the way down to the sole of your foot (it "tacks down" at the tib and becomes one wall of the anterior tib compartment, then tacks down again and becomes part of the "stirrup" in the arch of your foot) so she should show you how to stretch and release it all the way down.
There is also a branch of the ITB that wanders over to the kneecap and yanks it to the outside of the groove it runs in. If the rest of the ITB gets cranky it can give your kneecap fits, too. So have her teach you how to handle that.



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