Pain: nerve vs muscle vs joint?

Is there a specific pain you are wondering about? I have spondylolisthesis in my lower back. I also have severe "osteoarthritis" with severe spinal stenosis in my lumbar spine. I suspect the damage to my lumbar spine was actually the result of "inflammatory arthritis" but the pain is probably the same. The only difference is that inflammatory arthritis is caused by an autoimmune condition that flares up for no apparent reason. Osteoarthritis results from a traumatic injury of overuse of the muscles and joints. Osteoarthritis is called "wear and tear" arthritis as we age.

I would guess that your "achiness in my lower back around the back of my waist" is more likely osteoarthritis. However, an exam by your doctor and an x-ray of your back would be better than me guessing.

I would agree that your "stabbing pain in the back of my knee" is likely the result of nerve compression. There are many nerves running through that area. of the knee. One nerve in particular that I know about is the peroneal nerve it runs in that general area. Compression of that nerve can cause the condition of foot drop. I'm told that women are prone to this injury more often than men due to crossing their legs too long.
https://www.mayoclinic.org/diseases-conditions/foot-drop/multimedia/peroneal-nerve/img-20008172
I'm not sure what caused the injury to my peroneal nerve but they say my peroneal nerve damage is permanent. My foot drop has persisted for 5 years.

Nerve pain is usually described as "stabbing" or "burning" and sometimes "electrical" pain.

Radiating nerve pain travels down the length of the nerve. That pain tends to hurt in places like your foot but the nerve compression is in your spine. Nerve pain is very tricky. The pain can be in one area but what causes the pain can be somewhere far away from the pain.
https://www.webmd.com/pain-management/ss/slideshow-neuropathy

On the affected knee if the pain behind your knee occurs mainly after walking, check behind your knee by palpating the area to see if it’s swollen. My father in law had similar symptoms and it was a Bakers Cyst, which you should google and check out.Sounds like all your other symptoms are coming from your back spondilo.. and arthritis in your low back. You should have it checked out though especially if painful too often.

I have spondylolisthesis as well as arthritis at L4-L5, I don't see how one could tell which condition is causing which symptoms. Had L-5/S-1 fused a couple of months ago along with removal of a cynovial cyst. Arthitis caused the cyst which was pressing on S-1 nerve root.