I am so sorry to hear your news!! I had some mysterious things going on with my neck for about 3.5 years a while back and the hardest thing was not knowing what was going on and not getting direct answers from doctors. The thing that finally helped me to get back on track and back to exercise was a physical therapy/massage therapy technique called Cranio-Sacral Myofacial Release. It seemed that I would be icing/heating, taking advil and rubbing arnica gel on myself forever and forever dependent on P.T.'s, and chiropractors, ever afraid of the tiny movement (I once threw my neck out brushing my teeth, another time I did it reaching for the mouse to my computer)that would make my neck "go out" again. CSMFR really helped and in a very short time, it was both a great short term and long term solution. My neck never bothers me now, and I workout all the time. I never thought I would have my life back...I know that different things work for different people, and you don't even know what is up with your knee yet; but the PT schooled in CSMFR can be a really helpful diagnostician where sometimes the MD's are a bit mystified by the musculo-skeletal stuff.
Hang in there and best of luck! I know what it is like to experience the pain, frustration, and fear of having your body become unpredictable. The one thing I hung onto was the firm belief that activity was the solution and not the problem and I kept searching until I found a healthcare practitioner who was also firmly entrenced in that belief. I wish I could help, as though you don't know me, your workouts have helped me so much! Coming back to fitness with a weight problem after years of inactivity was SO HARD, and you and your workouts really helped me to hang in there. You are an inspiration and a gifted fitness expert.