Is it possible for knee pain/swelling to now start also causing pain up thighs and painful lower back - or are they 2 totally different things?

Possibly. Painful knees can cause you to alter your gait. Often the altered gait can then lead to hip and/or back pain.
Probably back issue. This is likely a manifestation coming from your backand radiating to your knees and not the other way around. Motor and sensory testing would help differentiate. Physical therapy will likely help you.
Many possibilities. The knee is an important weight bearing joint with a complex inner and outer structure. Your pain could be as a result of many different things. A thorough history and physical exam and possibly some laboratory and radiology exams are needed to determine the exact cause. Causes of pain may include: trauma (fracture, tendon or ligamentous tear, arthritis), infection, and metabolic conditions.