I'm hoping to do the JMT again this summer; permitting doesn't seem to be much different from before:
"John Muir Trail area Permits:
Required since the routes are thru National Parks or wilderness areas. Get the permit at the point of entry. East side permits are U.S. Forest Service. The Mt. Whitney end is thru the Forest Service by lottery, but there are nearby passes where you can get to the JMT and permits are usually available in advance or at the trailhead. Try to get them online as there is a daily quota at all trailheads. Forest Service Permits. Sequoia-Kings Canyon National Park Service Permits. Yosemite National Park Permits. Starting from Yosemite on your online reservation request, entry trailhead will be HappyIsles>LittleYosemite and exit trailhead will be Lyell Canyon. When you pick up permit, tell ranger your final destination is Whitney Portal and approximate date of exit. Ask them to stamp it for the Whitney Zone! If online reservations are full for your day and route, do not be discouraged. 40% of permits are reserved for walk ups either for same day or one day before. Go midweek, get in line at the wilderness early, and have a day or two flexibility. If the Happy Isles - Little Yosemite is still full, ask for Happy Isles - Sunrise/Merced Lake - it works for JMT. If you still can't get a walkup permit, try for one leaving from Tuolumne Meadows or Glacier Point."
You can request your permit 24 weeks in advance. Good luck on your hike... maybe I'll see you out there!