What is the clunking noise and shifting noise I hear in my knee? It is very painful something is moving I don't think it is kneecap. What could it be?

Get seen. You have 4 separate posts about meniscal roottear, osteochondritis dessicans and tibia slipping- the possiblities are too broad to figure out online, you need to have a open discussion with your surgeon - he or she knows your knee better than anyone else on earth and can address specific questions about the mri. Seek a second (not 3rd, 4th and 5th) opinion if you arent satisfied with the answer.
Cartilage tear. You can have have locking and popping of the knee if you have a tear of the meniscus. This shifting can cause pain and in some cases swelling. Exercise can help. You may want to get an evaluation. See a sports medicine physician first to get an exercise program.