Recent RA Diagnosis with some questions

I was recently diagnosed with RA and put on methotrexate, hydroxychloroquine, and folic acid.

My symptoms were generalized pain in hands, feet, wrists, ankles, knees, elbow, hips, shoulders, and neck. I also have pain in the muscles around the areas. My Doc's initial impression was fibro, but I have a family history of RA and I was also exposed to the burn-pits in Iraq which has been loosely linked to some immuno problems that don't normally occur. I'm a 46 yr old male.

My blood tests came back with positive ANA, and a 22 for the RA Factor (up from an 8 two yrs ago), and my sed rate was off but I don't remember the number. My x-rays and MRI all look normal though so I'm wondering where the pain is coming from? The MRIs don't indicate any inflammation or degeneration at all. So I'm kinda wondering if we might be treating the wrong thing.

I'm also still in the Army and going through a Medical Evaluation Board because of the methotrexate and some other medical issues. MRX makes you non-deployable, so not fit for duty. But the VA Doc (not a Rheumo) was questioning the diagnosis because there is no damage already since we caught it all very early. Am I crazy? Well don't answer that, technically, I am - but is just the blood test enough to accurately diagnose RA or might we be treating the wrong thing?

Yes, we looked into Lupus too but that isn't it either. Initially we were thinking Fibromyalgia but when he saw how much my Rheumatoid Factor had gone up in two years he went with RA. I'm scheduling an appointment with him to go over some of the additional test that the Veterans Affairs likes to have on file (probably some that involve a cauldron and leaches the are so 18th century).

When I first began having symptoms I was having extreme pain in tendons and muscles surrounding my joints but not having any inflammation of the joint itself. This went on for almost 3 years before I began exhibiting typical RA flares in the joints and I had no diagnosis leading up to this point as well.
It was only after I had my knee flare up badly that the blood work showed the severely increased rates. They took fluid from the joint as well and tested it for RA factor and only after this would my doctor refer me to a Rheumatologist.
It was a very hard time for us as I was no longer able to work due to it but with no clear culprit or treatment plan to get my life on track once again.
Hang in there and keep a daily log of your symptoms along with writing down any questions you have for your doctor. If you are able to I would get to a rheumatologist in addition to your regular doctor. Once I was able to see a rheumatologist she was much more versed in the specifics of AI disease and the markers for RA.
I hope that you feel better soon and pray your symptoms subside and never return. Hang in there and don't give up hope. Many of us have had similar situations and while difficult we were able to get through them and remain productive for many years although maybe not in our chosen fields. My personal experience has been that The Lord has provided for me even in my darkest hour when I could see no path to weather the storm. I take comfort in that every day. Thank you for your courage and self sacrifice serving our country!