I hope the MRI will give you and the dr some more information.

About the kneecaps & possibly some of the other muscle aches and pain - have you checked for hypermobility?
http://www.hypermobility.org/beighton.php

If nothing is definite on the CM after the MRI - make sure they check it for extra cervical ribs.

So many of the symptoms you mention could be from something like thoracic outlet syndrome {TOS}also.
here's a good info link-
http://www.medifocushealth.com/RT017/index.php
and more
TOS sticky thread-
Our Useful Links - Websites, Articles & Polls
http://neurotalk.psychcentral.com/thread84.html