I was frustrated for my first year with the Army medical system. I was having issues with lower back, shins, ankles, and feet; profile for 6 months no run, just new to the unit. I was considered a dirt bag. My PA was some old guy who didn't take time to listen, sent me for x-rays and bone scans on all parts of my body. It wasn't until I got a second opinion from a Doctor who listened, happed to be a specialist for sports medicine, that I was correctly diagnosed with a common foot problem. I was issued orthotics for both feet and ran the next day and haven't stopped since. That was 8 years ago.
Just remember, a military PA is just an assistant, a Doctor in training. All of them. You can request a second opinion from your primary care provider or just ask for a referral to sports medicine or some kind of specialist. Bone scans and MRI's don't cost that much in the Army, we own the equipment and most of the time the technicians are military. Don't take the cost as an excuse for not getting the medical attention need.
While you are working on getting the help you need, you may also want to talk to a running coach, sports doctor, or someone who is well versed in those areas. You describe common issues with running with wrong shoes, bad stride, or over use injuries. It is no shock in the Army that someone would have those symptoms. From personal experience with some of those issues, lots of ice. Take an ice bath, I know it is cold, but well worth it.
Unfortunately, getting medically removed from service doesn't take a whole lot. When the documents are sent to the medical board, it is up to them to decide. While I was a Drill Sergeant, PVT's were getting out for the smallest of issues. Just ask, request, and follow up constantly with your PA, it shows you care and will keep them working. If they are dragging their feet on the issue, talk to your 1SG, they seem to have the magical phone number to getting things done when you hit a brick wall.
My psych-team doesn't really listen. They'll up my meds, or give generic advice. Nothing specific. I'm a Veteran with CPTSD and other mental and physical problems. I've been getting steadily worse since the latest psychiatrist took over. He's the latest, in a very long line of them.