Dear Moonunit

your hypthesis sounds quite logical, why dont you test it by having someone tape your patella into good tracking then go for your bike ride...if you do not get pain as you usually would feel with the usual, then this is the problem...and you dont need anybody's advice here...

your description trully supports a patella tracking problem, especially with the stairs bit...if your femur naturally falls into external rotation, one can only imagine what is happening to the femopatellotibial alignment...

you can assess yourself

place two fingers one on each side of your patella as you long sit...try to keep your lowerlimb as straight as you can, push the back of your knee down, your patella should glide horizontal in a straight line, does yours deviate anywhere? medial, lateral?

ask a friend to hold your patella down, the push your knee down to contract your quads, the pain you feel is it similar to the ususl pain you get when you ride?

test the length of your ITB on both sides...also test the lenth of your quads and hamstrings on both sides? any difference?

you hip cracks and pops? you might have a snapping tendon there or torn cartilage? perhaps too much anterior glide in the hip with external rotation? do you have a range of motion restriction as well or range is full?

what happens with hip flexion? any pain? what happens with resisted hip flexion? now what happens with a downward pressure on the anterior hip with hip flexion? any pain increase or decrease?

there are specific exercises to manage these problems

snapping and popping is unlikely to show anything on xray because it sounds soft tissuey...go for an Wikipedia reference-linkMRI instead , how old are you though?

cheers