it sounds like patella femoral syndrome and the crunching noise comes from the fact you have rough cartliage. Squatts probably arne't such a great idea atthe moment because of the strain they put on the kneecap. Cartliage wear can be picked up on mri but it isn't 100%, it can be very vague infact I would suggest asking the pt if your knees are tracking and see what they suggest.
if the knee is tracking OK and still making the noises it is the result of the rough artliage and the only way you can get rid of it is by having a scope and getting it smoothed off. A smooth surface will not wear away as quick as a rough one so it will buy you a few more eyars before arthritis sets in.
I hope all goes well and you pass the physical and are able to get it resolved because all those runs and marches will be very hard on the knees.
Best of luck