You can pick up the trailhead at the west side of the Tuolumne Route # 120 bridge in the meadow at the car camp entrance. Just follow the river all the way back through the campground proper and eventually you will see there is a small JMT sign at the very end of all the campsites. You can also start at the Tuolumne HSC, or go straight back from the permit area too. The many trails there eventually merge into one, and it is just across the creek drainage and it follows the Lyell upstream for more than a few miles.
It also is my understanding that for JMT "through hikers", if you obtain the permit in Yosemite, you can automatically exit at the Portal (The official Trail does end at the summit) or down the MR if so desired. You could also exit at Horseshoe Meadows if you so stipulated this when you got the permit. Ran-gers are usually good people, and realize that you have to be able to get down and finish someway. In addition, seeing as you do possess a legal JMT permit, and the conventional trail ends at the Portal, there is also no need to put down an exact exit date as they realize that this exactness to detail is impossible to keep to, starting 3- 4 weeks beforehand. This “unofficial” courtesy seemingly only extends to JMT through hikers with valid permits only, and the Ran-gers have always cut those doing it some slack, for completing the entire trail._ (at least they did for me- twice now.) While I am at it, let us say thanks to them- again- for always being so understanding of us JMT hikers. I never had any problems with any of them, after I had the official permit in hand.
Mark
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