So the good news is that there are no tears or rips in my knee. The only thing Dr. Bruno could find wrong was a slight case of Chondromalacia AKA "Runner's Knee" which may not be responding to the ice and ibuprofin because of my weekly doses of Interferon.
So I am going to start 3 weeks of Physical Therapy to see if we can strengthen the muscles around the knee, solve some of the "Runner's Knee" and get the swelling to stop happening. After 3 weeks of PT, Dr. Bruno says "We'll see were we are at!"
In terms of activity, he asked me to wait until I saw the Physical Therapist so that she/he could determine how much activity I should be doing. In the mean time as long as I wasn't having pain I could swim or bike - NO RUNNING for now.