The only complication with later (after Sept 15) thru hiking will be the shutdown of most services - the resupply spots will be closed for the winter, so then it's a game of finding other hikers or packers to bring in your food resupply - or of carrying everything for the whole duration. And then getting to the end of the trail and finding a ride back to town.
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"In the beginner's mind there are many possibilities. In the expert's mind there are few." Shunryu Suzuki

http://hikeandbackpack.com