Zzz Factor V deficiency is usually associated with hemorrhagic complications but it can be converted to either a pro-coagulant or an anti-coagulant. Thus, this deficiency can lead to hemorrhage or thrombosis. In either event, the persistence of (what your description suggests) pleuritic pain, for over a year,following a pulmonary embolus (PE) is most unusual and could be on the basis of what is referred to as neuropathic pain; that is, pain secondary to injury/inflammation of one or more nerves adjacent to the (PE) or what may have been a pulmonary infarction (infarction = death of tissue). As you note, “sounds like I have some nerve damage from the blood clot.”
But it is also possible that this particular pain is not directly related to the PE but, rather, is associated with the “severe pain all over my body”, possibly as you suggest, secondary to fibromyalgia. Attempts should be made to distinguish between the two scenarios, for if the back pain is neuropathic, rather than associated with a systemic process such as fibromyalgia, the treatment of it could involve a permanent (intercostal) nerve block. It is even conceivable that you might, at any given time, be experiencing thrombosis and/or hemorrhage and either could be responsible for the chest/back pain.
The reported 48 hour monitor heart rate of 160-180 (tachycardia) with what sounds like minimal exertion, is very worrisome and very abnormal, especially for a young person. There are many causes of tachycardia but in your circumstance, major considerations would include recurrent pulmonary emboli, pulmonary hypertension, or a primary rate/rhythm disturbance of the heart.
You appear to have several, perhaps unrelated problems: 1) an unexplained rapid heart associated with shortness of breath, with minimal exertion, 2) chest pain, at the site of your lower lobe PE, that could be secondary to nerve (nerve root or intercostal nerves) compression/inflammation or, alternatively, a manifestation of, 3) fibromyalgia to account for the total body pain you describe. Yours is a complex problem, the diagnosis and treatment of which will likely require the concerted efforts of several specialists.
You should definitely seek consultation with a Rheumatologist, preferably one with much experience in the diagnosis and treatment of fibromyalgia. He/she may also wish to consult with a pain specialist in an attempt to sort out the root causes of your multiple pains.
You should also consult with a Cardiologist, preferably one with experience with pulmonary emboli and pulmonary hypertension, although treatment of the latter often lies in the purview of a Pulmonologist.
While one or more of the specialists may be able to sort out the causes of your several medical problems, you might do well to seek medical assistance at a major medical center such as the Mayo Clinic or the Cleveland Clinic. If you choose, instead, to be seen at the nearest University Medical Center you might want to proceed in a stepwise fashion, first seeing the specialist most likely to be able to provide an explanation for the tachycardia and limited exercise capacity, then a rheumatologist who might be able to sort out the causes of your near universal pain, and then finally if you have not yet achieved significant pain relief, seeing a pain specialist whose expertise could encompass multiple body systems.
Once again, yours is a very complex medical problem, one that might only be resolved at a major medical center, with physicians accustomed to seeing the unusual.
Good luck