this is actually an old thread, I completed the trail last august.
Like you said, the majoraty of the trail is on well maintained trails, and the off trail section above Clark Fork Meadow was one of the highlights of the trip. The trail ends in the meadow, so we had to climb up onto the ridge. It required some route finding, but the veiws from this section of the trail to St. marys pass were spectacular. This ridge was very easily followed.
The problems that we encountered were in the valley below 4th of July Lake and after summit city creek, the trails were completely overgrown and somewhat abandoned, and the walking along th mokelumne river was extremely difficult because it was surrounded by rock and boulders. the trail was marked my small stacks of rocks (ducks) be even still, it was very hard to follow. It requried some moderate-dangerous bouldering and bush whacking in this valley. and the climb out of it was probably the steepest of the trip, and there was a large feild of ice at the top, so we ended up having to go around it (we dident have crampons or ice axe) which required us having to traverse the slope, which was fairly difficult and dangerous considering the grade and us not having anything to arrest a fall.
but in the end, It was a great trip. other than about 18 miles it was on great trails. And I enjoyed the experience of the sierras.
Ive heard something about a Sierra High Route.
Im thinking about that for the future, it sounds simmilar to the TYT, just more southern, into the High sierra.
Please check out the gallery from the TYT