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.