You can start from the Tuolumne Campground, the Tuolumne Wilderness Office, Tuolumne Meadows Lodge or the Dog Lake parking lot, depending. All of these are roughly the same distance, but it's probably easiest to just park at the Wilderness Office, get your permit and start walking. Please note that this is a quota trail and there is no camping in the first four miles, so you don't want to start too late in the day.
You start out along the Dana Fork of the Tuolumne River, crossing that in about a half mile. It's about another .75 miles to the Twin Bridges over the Lyell Fork of the Tuolumne River. Here you meet the John Muir Trail proper, which is also the trail from the campground. The Twin Bridges area is a gorgeous site — nice meadows, gracefully formed granite cascades and views off to Mammoth Peak — and worth a quick walk in and of itself if you are just spending the night in Tuolumne.
In another half mile, you come to a trail junction. The righthand branch takes you up Rafferty Creek to Vogelsang High Sierra Camp in 5.7 miles. Our hike stays left on relatively flat ground that alternates pleasantly between lodgepole forest and meadows. You'll eventually arrive back at the Lyell Fork and soon find meadows, shade trees and rock bluffs that all call for a break. At the first small outcrop, one day I saw a man fly fishing off the outcrop, hikers having lunch, a man with a hammock strung between two trees, and some folks dipping their feet in the creek. All in all, it's a shame to move too quickly through here.
You are now in the large meadow created by the Lyell Fork basin. Across the creek is the Kuna Crest and on trail side, Potter's Point looms ahead. You will leave the river and then rejoin it again. A little further on you are out of the no camping zone and there are lots of established campsites in the small groves just up and right from the trail.
About six miles from the start (4.2 miles from the last junction), you reach the Ireland Lake Trail, which takes you to Ireland Lake, of course (4.3 miles), but also to Vogelsang High Sierra Camp in 6.3 miles. So if you wanted a nice loop, you could head to Vogelsang that way and then end up back at the previous junction on your return trip. Above you, Potter's Point provides a handy mileage marker reference point for the remaining miles in the canyon.
In another three miles or so, you reach the head of the canyon, where Kuna Creek comes cascading impressively down the mountainside. The next good campsites are a ways up, so if darkness or fatigue are coming on, this is a good place to stop. That said, you never go too far between camping opportunities and water is common along the trail.
From the head of the canyon, you enter steeper, more forested terrain with white heather giving way to mountain heather and, eventually, lodgepole pine giving way to whitebark pine. About 1.5 miles on, you come to a crossing of the Lyell Fork, now a relatively small stream, but fresh from the glacier and bracingly cold. You now wend your way up steep slopes for another half mile, emergine at about 10,500 feet with nice views of Mount Lyell. Where the trail takes a horseshoe bend at the crest and head down to cross the stream and then up and over Donahue Pass, summit-bound hikers leave the trail and start up the shallow canyon straight towards Mount Lyell. The rocky subsidiary peak you see between you and the summit looms at aobut 12,400 and is a good measuring post for your progress. Easiest is to work your way up and right around the foot of that peak, passing it on your left. From there you can either kick your way up the steep snow slopes on the north flank of Lyell or wind your way around to the southeast flank and scramble up easy third class terrain to the summit. The northern snow slopes are more spectacular and more amenable to taking in Lyell and Maclure in one outing, but also more difficult and dangerous.
The summit of Lyell can have incredible displays of Sky Pilots (Polemonium eximium) if you get lucky with your timing. In mid-July we saw thousands of American Lady butterflies pollinating the Sky Pilots and being in turn eaten by a bird that we didn't get a great look at.
In any case, it will have excellent views of its neighbors, Maclure (12,880), Mount Florence (12,561), Rodgers Peak (12,978) and further peaks like Banner (12,945) and Ritter (13,140). You can also see all the way over to the Buena Vista Crest and Horse Ridge above the Ostrander Ski Hut.
From here you simply trace your steps back down. If you came up the snow slope and are travelling light (i.e. without ice axe and crampons), you will likely find it more comfortable and quicker scrambling down the rocks heading towards Rodgers (SE ridge). Of course, if the snwo slope is not suncupped and you have an axe and are ready to glissade, nothing's faster that going down a nice snow slope. Typically, however, by the time the highway and the trail are snow-free, everything will be suncupped and not a very fun glissade.