It sounds a lot to me like you hurt your spine rather badly in that bike accident. See, some of your list of problems has to do with where the nerves go from the spine, which the ones affecting your hands and fingers and thumb come out of the cervical spine, and then the ones affecting your blood pressure and breathing and the pain between your shoulder blades come out of the thoracic spine, normally T-5 and above, which T-4 is about where the actual nerve injury is since it's always felt one vertebra down at T-5. Don't worry about your knee right now, aspirin should keep it from bothering you too much, and you can buy a simple elastic brace to go around your knee if it's too rough one day or whatever.
I'm assuming your MRI was of your head, they may have thought all your symptoms come from a brain problem or concussion, but since that turned out okay, then I'm thinking you need some sort of scan of your cervical and thoracic spine. It could show some sort of damage to the vertebrae, discs, or nerves in there, and any in your thoracic might explain your breathing problem, which seems to be the one most affecting your status in the military.
So, I think one of your next steps is to get at least a black & white X-ray of your neck and chest, or a CT scan or MRI, depending on what doc you visit wants to do. Also, you should ask this doc to review the radiology report from your brain MRI. If you can get in to see a neurologist fairly quickly, that's who I'd go to.
In the meantime, another step is to practice deep breathing, breathe in really deeply, blow it out fairly slowly, breathe normal a few times, the deep breathe again until you've done it a half-dozen times. Do this several times a day. Also, where you feel that pain in your back, if you can get your wife or a girlfriend to massage your back between the shoulder blades by pushing on either side of your spine firmly but gently, that could relax those muscles and unkink those nerves after a few days of that. And anytime you're sitting and watching TV, put a hot water bottle in that area.
THEN measure out by your car a mile and a half or figure it out on a track, and then just WALK and jog a little that distance. If you're jogging and it begins to hurt, go into walking and deep breathe and watch your posture so you're holding yourself up really straight as you do that, shoulders back, and then when you feel like you've caught your breath and the pain diminishes, pick up and jog again for a while. If at any point you cannot stand it, go lay beside the track and then quit for the day. Next day, go out and practice again. Do this until you can arrange yet another running test so you can stay in the military.
Let us know what happens, keep us posted.