How does one navigate the VA healthcare system to get treatment?

You will need your VA PCM order it. Doing it through the VA PCM will ensure it is in their system. Basically, if you haven't been seen by the VA for it before, you need to begin getting seen for it so you can develop a history. After "X" amount of visits and "step-up" treatments, one of those steps will be an MRI, since you already have the X-ray accomplished through the VA (baseline)... Its odd, but their treatment seem to be based on progression and in-order-treatment-sequencing... But you definitely have to build a progressive history with them for that issue, and this doesn't happen over night. This is just my opinion and my VA experience. I hope it helps.
Oh... And patience... Don't forget or become frustrated with the patience...

I just refused a VES exam for a GI problem. They contracted with a PA with 1 - 5 years exp. There is enough in my file to make a dec.

I refused C&P at VA for my knee a few weeks ago because my knee had a C& P exam in August 2017. i also had a July MRI from my knee doc. They granted me 10% on my knee back dated to the MRI it took a few days. I was shocked. My last claim for my other knee and shoulder increase took 4 years.

I am starting to believe the VA folks who gather the evidence for the reviewers follow some type of checklist without paying attention to your medical evidence.

i also don’t trust contractor exams. if there medical evidence in you file supporting your claim consider skipping the exam and requesting an immediate decision. I know they scare you about refusing exam but if there is evidence in you file supporting your posn they have to consider that evidence.

Talk to a good atty or a good VSO if you can before making a decision. I am confident in my case that the BVA will look at the VA and wonder why are you sending a vet to a PA for a GI claim.

If you had paperwork upon discharge saying that you needed an MRI for tendonitis in your elbow and upon checking in with VA you only got an x-ray and found nothing, you need to get a patient advocate which are at the VA installation to plead your case for you.