Have an MRI done. I experienced the same for years. When I finally saw an orthopedic surgeon the found bone fragments digging into my nerves and missing carlidge. I now am going for carlidge replacement surgery in May. This will help avoid a knee replacement. I'm only 45. I've gained weight because of all I'm limited to. Definitely see a doctor!
Could be Vitamin D deficiency. I have got that and my shin bone on the left has been getting shooting pains and gnawing burning pain in it as if I had picked a scab off of it or cut it even. Bloodwork came back normal. So it leaves me to believe it's the lack of vitamin D. I don't drink milk and I stay inside out of the sun. Sleep by day and awake at night. Recently read that almost all of us do not have the amount of Vitamin D that we need. I would recommend adding a good otc multi vitamin into your diet. Or one of those hardcore 500 mg Calcium vitamin D pills or both! Hang in there and hope you get everything situated.
You may have arthritis in your knees. I suggest taking Magnesium and Calcium and D3. You don't say if your knees are swollen, but elevating your legs when you lie down will also help. Squats are not the best exercise for you at present. Walking is safer and not so hard on the knees. - See an orthopedist or rheumatologist.