I can’t speak to JMT conditions in August and September, but as for the CT, put these facts into the decision hopper. In August in Colorado, you’ll be in the heart of what locals call the monsoon season. Afternoon rainstorms, and more importantly, nearby lightning strikes are daily liklihoods, not just possibilities. The storms rarley last more than an hour or two, but they are very violent while they do. So in August, you have great temps but potentially dangerous conditions on the exposed ridges and mountain tops. In September, the lightning storms subside and the leaves begin to turn every absolutely gorgeous shade of orange that you can imagine, but the temps begin to drop and the possibility of snow storms increase. Just last week nightime lows were already down into the high 20’s and I discovered 7 inches of snow when I popped my head out of the tarp at 11,000 feet near Silverton. The conditions I later found up on the trail at 12,500 feet were almost impassable. Two days later, and another round of the white stuff hit. Kind of unusual, but clearly not outside the realm of possible. So September again provides great hiking conditions but also the threat of storms, albeit of a different nature. Considering all of the above, if it were me making the back-to-back hike you’ve dreamed up, I’d rather do the CT in August. By the end of September, I think the trail would just be a little too cold for me to enjoy.
Matt