Justin, I usually feel the altitude around 9,000 ft, after about 2 hrs at that elevation. What has always worked for me, even when coming from sea level, is tons of hydration. I drink water the day before I start, the morning of, every hr etc. Combine that with proper nutrition, and being in decent shape to boot, and you'll be good. I don't remember the science behind it, but I've read that those in better shape, potentially deal better with altitude. Since you plan on doing the JMT, you'll likely want to train at least 3 weeks to 1 month for it), so your starting condition should be fine. Also, I pop 1 advil if necessary. It also helps if you can spend the night at moderate elevation the night before. I slept in Mammoth Lakes, CA (elevation ~7,900ft) the night before my JMT, and I think that helped.
Worse case scenario, get a prescription for Diamox