I also just finished a thru about a week ago. I went SOBO, resupplied only twice, sixteen hiking days and one zero day. I agree with Jake-- the north isn't actually super hard. Going over Camel's Hump and Mansfield are probably the toughest. I started out doing mostly 20 mile days from Canada all the way to Mansfield, and found it to be pretty nice. I know you're a fast hiker, so I think you'd be fine.
Bugs in September? No. Just worry about ticks, but black flies and skeeters won't be an issue.
Temps? My guess is it could drop into the 30s at night. Generally, the first snow in the mountains is in early October (a good reason for going SOBO in the fall).
I resupplied at Jonesville and Inn @ LT (both right on the trail, if you take the old LT route to the Inn), but getting into Johnson and Manchester Center for resupply also wouldn't be too difficult, and they're good towns. I heard Johnson was particularly friendly to hikers.