Pulmonary Embolism Support Group
By far the most common form of pulmonary embolism is a thromboembolism, which occurs when a blood clot, generally a venous thrombus, becomes dislodged from its site of formation and embolizes to the arterial blood supply of one of the lungs. Symptoms may include difficulty breathing, pain during breathing, and more rarely circulatory instability and death.

I believe the standard therapy for a first PE is 3-6 months on blood thinners then nothing (no D-dimer tests either) unless something else is going on. I believe the D-dimer does not have a lot of value as a standalone test in the absence of symptoms, my understanding is that they just use it to see if they need to check out your symptoms further with the more expensive and invasive tests or if they can rule out a clot.
So. If it were me and I had no symptoms and no medical reasons to be on the bloodthinners indefinitely I would just do what you're doing but drop the monthly D-dimer (but get one if new clot symptoms pop up).
I believe body aches can be related to depression.
Teristalking2u, maybe look into some kind of physical therapy. If you have pain in your bad knee, you have probably been compensating for that with your other leg which can affect your posture, your gait, etc. That could all cause pain elsewear.