I had a patella re-alignment & scrape on my left knee about 10 years ago and recently had similar feelings as you described in same knee, so I tried altering my running tecnique, (the angle and flow your foot hits the treadly) made a big difference, however, now I am getting sever shin splints in my lower right leg.. Can't win..

But as others have pointed out, cross trainer + spin bike are way to go.. Vary speeds and resistance to build your lungs & heart musles will also help to build your stamina..

Zero to Hero takes time.... Just keep focued on the end game..
And well done TJ, blood & sweat sounds like its paying off..

By the sounds of it we should start a PWRX biggest loser!!! Few of us have a few (10-15) kg's we'd like to lose!!!