There are a lot of causes for knee pain.
The knees can compensate for bad posture, a bad hip.
There is a limit of course, as real damage begins to occur to the knee due to too much stress.
The business about kidneys and the left knee is interesting and wouldn't surprise me if they were interrelated.
In your case I suspect you have a slight case of Osteoarthritis.
The fact that your knee got worse with yoga then jogging (your doctor was an idiot for suggesting jogging if you experienced pain with yoga) suggests you have sharp areas of bone within the knee.
These are shredding your cartilage.
My wife had orthoscopic knee surgery a few months back.
The pictures were amazing.
Her severe pain and inability to bend the knees without pain, was brought on suddenly by us redoing our back yard garden area.
She literally shredded the cartilage (getting up and down on her knees) because of the bone being jagged.
I suggest you see a knee specialist and rethink your exercise routine.