OP-as you can tell there could be a number of possible causes and thus a number of potential solutions to the knee pain problem. If the pain is near the top of the patella "usually" that could mean a couple of things...well several actually. For one are you pushing a much harder gear than you are used to instead of spinning at 80-95 rpm.
If it is a fit or position issue, usually it is because the saddle is too low or too far forward. If it is just one knee hurting, the first step I take is to move the cleat that foot closer to the arch (this lengthen's the leg reach for that leg). If it is both knees then you might raise your saddle a couple mm's as the first change. Don't do a lot of different changes all at once. Start with one and see how it goes and then make additional adjustments as needed.
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