Reading all of your accounts is sounding familiar. It's surprising how many of us suffer from knee problems at one time or another. Right knee pain flared up with me in early 2010 after a year or so of slowly increasing niggle when I hammered the downhills, but it only flared up properly when I had to stop running due to a broken foot. Before I knew what I know now - that it was tendon inflammation underneath the kneecap - I thought it was the end. Rest made it worse and sitting was the worst of all. I couldn't keep my leg bent at right angles. My comeback began with the LDWA 100-mile walk/run in Scotland. The long-term gentle exercise and stretching over 34+ hours brought relief I never dared imagine. I could sit in comfort again. Tendons are funny things and they don't like total rest.
I've had a knee niggle recently which seems to be getting sorted now. I've found this web site- mobilitywod.com really useful. Do a search for knee and all sorts of ideas come up, some interesting ones too.
I've been having shockwave therapy on my kneecaps which seems to be working, and the rowing machine is good for coming back. I've got to go for a 20min jog on sunday, flat.