Vitamin D/B12 deficiency, knee, hand

I have been diagnosed PFPS with patella alta through MRI in the last October. Going to PT from November. The burning pain above the knee and little swelling above the knee is still the same. No improvement in the symptoms. Tried one session of dry needling in my quadriceps too. No changes in the burning pain and swelling. Recently got burning  pain in forearm, wrist and elbow area. Dr says mild carpel tunnel/mild tennis elbow/shoulder bursitis. And says that is inflammation and prescribed diclofenac sodium DR tablet75 mg twice a day for a month. I am going to PT for my hands and knees now. I don't know how long does my knee take to recover. It's been 5 months of this burning pain. Is that normal to have burning pain so long? What else to do to recover? My vitamin D is 19.1 and b12 is 406. I have low iron saturation. Taking iron supplements 3 times a day and D3 50000iu per week. No supplements for b12. Is this vitamin deficiency related to the joint pain or inflammation?Is it related?