I tend to favor hiking the first few weeks of July because it tends to be less likely to be stormy. But Sept. is similar. I don't recall having problems with mosquitoes on any of my JMT section hikes, and nearly always hiked in July.
I hiked north on the PCT out of Tuolumne Meadows years ago, and we expected (and encountered heavy) mosquitoes. We were prepared, though: mosquito head nets, and a spritz of high % DEET repellent back of the hands and any thinly-clothed areas. When mossies were heavy, we just hiked on until we found a drier (and mosquito-free) spot to camp.
