OK, here's what ended up going down.
I saw the flight doc about a month ago. He checked me out, took some x-rays, the usual. He said he noticed some thickening in the hard portion of my tibia, and that this was a telltale sign of impending stress fracture. He told me to not run for 2 weeks, and put in a referral for orthotics.
I cross trained regularly. Rode the spinning bike (fast, light load) and did some time on the erg and in the pool to stay in shape. Everything feels good now---I'm going to try running tomorrow at A-pool PT.
The referral process was a little annoying. The doc said it would take 48 hours for the referral to go through---it took over two weeks. I had to call central appointments and tricare to get things sorted out. Went to the orthotics place out in town and they took imprints of both feet. The new orthotics will arrive in 3 weeks.
I asked about the rigid versus semi-rigid vs flexible orthotics. For distance running, you want something that is pretty rigid to maintain your arch. The more agility based your sport is (football, basketball, etc) where you have lots of lateral movement, the more flexible you want your orthotics to be. My new ones will be made out of hard plastic from heel to arch, and foam at the forefoot. The whole orthotic is covered in foam so it's easy on the foot. My old ones were the same way, and were very comfortable.