im going to have to agree with Marj here. Patella tracking is a rather complex motion, first of all its not possible to see how your patella tracks on an MRI. secondly, tracking of the patella is relative to the assessments being made...i.e, your patella can track properly but still not effectively, for instance it may be tipped superiorly, laterally inferiorly etc...so your consultant may have overlooked its alignment when he or she checked its tracking.
you have described areas of discomfort akin to the patellofemoral ligament mainly...meaning you are showing signs of an overuse of this tendon. The question is why? first of all the majority of your questions you have answered yourself, the adjustments on your bike sound like the would obscure the alignment of your patellofemoral joint anyways thus causing an overuse of this tendon.
maybe you should try to change the adjustments so that you have a better knee joint alignment. you do realise that you are of the age wherein tendon issues are most common...only because you start to lose your flexiblity often mainly as you approach the middle ages...
there are knee supports that relocate the patella, and there are taping techniques that do the same, maybe trying out all these measures will stop your symptoms from emerging however if they are showing now, it is likely that no matter hopw much physiotherapy you get in the short term, they will always continue to be an issue from time to time.
one of the things you have to worry about are the possibilities of future knee joint arthritis. the surgery you have done may have left your quads slightly weaker that normal...take time to gently exercise the quads in the interim.