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Question on Running and Injury Recovery

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Quick question regarding knee + leg muscle injuries - I have done a lot of distance running over the last 25 years (now in my late 30s) and had a pretty bad knee/leg injury which involved a lot of pain and swelling with walking and doing simple things.  I've gotten to the point where the x-rays are good, and there doesn't seem to be much progress in PT/chiro with what's left of the pain...


I can run 3+ miles without pain, I can jog up steps, bike, swim, etc etc.  But if I squat or do anything that involves a deep flex of the knee, there's pain - I was wondering if this sounds normal to anyone else and maybe it's just me aging normally, or is there a certain rehab program to try, strength training for specific muscles, etc?  


Thanks in advance! 

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I've been running healthily but I have significant knee pain when lunging or squatting deeply. I have loose cartilage and arthritic knees. Mostly from many years of being massively overweight (Until 2 years ago). I use Negative Split Squats to work on muscle building in the knee area without pain ( Here's a vid I made for NF on how to do them https://www.youtube.com/watch?v=Bx1TdZ418Yg ). Additionally,I fairly religiously follow Jason Fitzgerald's Injury Prevention For Runners program from Strengthrunning.com. Jason was the 2015 Camp NF running coach( So he's NF Approved ) and in my opinion, a running god. He keeps me injury free and when I did get injured ( IT Band Syndrome ), his program taught me to heal myself. I got the cheapest ( 50 bucks ) version and think it's well worth the money even though it's kind of a lot of money for a couple of eBooks.

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