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As far as that first CT scan and your positive D dimer, tachycardia and fever...I wonder if you did indeed have a PE.
I am not a doc, so please take what I say with a grain of salt...I have suffered what is called micro emboli,meaning that the blood clots that went to my lungs were very tiny and numerous. The only way the doc picked up on that was from my lung biopsy. The pathologist could see the tiny micoremboli in my arterioles in my lungs. At the time of my symptoms, they did CT scanning along with the typical tests for PE and they came back "normal"...my microemboli were missed by traditional testing. I too had tachycardia and low O2 levels (I have other issues that contributed to this, but they were more exaggerated at the time of my PE).
In my honest opinion, I think you need to see a new doctor who will listen to you. Nothing is more frustrating than a doctor who is so passive and not willing to explore why all of this is happening to you.
Good luck...Sunny