What Causes Swelling In Legs Along With Shortness Of Breath?

Hello, and thank you for taking the time to read my question. I am a 35-year-old caucasian male. I have always worked out, at least five days a week with moderate plus workouts. (I am extremely healthy, fit, and am by no means overweight.) Never smoked, but drink occasionally (1 or 2 drinks per week) Married, two young boys. In June 2015, my wife and I had taken a trip to Vegas for our anniversary. The entire trip, I felt a little tired, my leg had been bothering me for a couple weeks, but thought it was an injury from a CrossFit workout. I also found myself out of breath often from climbing the stairs. I initially was treated for DVT from mid thigh to below ankle...at least this is where the clots were located during the doppler...I then received a CT where they located another large PE. From CT to heart echo they found slight enlargement of right arterial. Immediate course was to begin blood thinners (Xarelto 30mg), but also did blood panel screening where genetic abnormalities surfaced (Leiden Factor V and Lupus). Since then, I have been on Xarelto 20mg per day. September, I had another doppler where they showed the clot had shrank... identified from below the knee to above the ankle. Time of diagnosis: Initial Symptoms - Charlie horse leg pain, swollen ankles and legs (both extremities), very poor circulation to feet. September: I still have fatigue, some swelling (drastically reduced), shortness of breath when working out. I did chalk this up to being away from the gym for a couple of months. (as prescribed by MD) Decided to order another CT for September and recheck with MD. December: PE was not identified in the scan, which is great news. Still slight swelling in legs and shortness of breath when working out. I am sweating a bit more than usual as well. (recheck with MD in February) February: Slight leg pain behind the knee. Slight swelling in both legs still and still shortness of breath while working out. Shortness of breath has never been a HUGE issue, just enough to know I am not myself and I am tiring too easily. Order for Doppler of Leg, Heart Echo, and Lung Function. I did go to the doppler today. The clot is still there...now understanding this will probably be permanent. I am now trying to understand where we are now and where we are going. I know I should wait to pursue any conversations until after the echo and the lung function with the cardiologist and pulmonologist, but I really want to get a good understanding of what is going on and the next questions I should have for both of my doctors. Since my follow up appointment will not allow me the time to think of potential questions ahead of time, I really would like to be prepared. First question to you - What questions do I need to ask my doctors? (Can I ask you guys this? lol) Second question to you - Am I under the proper medication for this and shoot I be looking into alternative course for treatment. I really appreciate all of your help. Thank you!