Dear Juseasy
I will be agreeing with my colleagues to say this is probably a systemic problem. As you are having localised signs in both knees, swelling etc its probably not related to the spine...you described night pains, with some description that indicates probably stiffness (feeling like you want to move it to ease the pain, swollen and tight)...any family history of this type of problem? any morning stiffness? have you done any blood tests to screen for R.A? your issue sounds like a connective tissue disease of some sort?
Maybe you want to shed some light on the exercises you were doing that you feel aggravated the problem?