I think the black flies won't be much of an issue by that time of the year. I just finished a thru-hike of the trial this month and they were only a problem for the last week or two of this month. There will still be mosquitoes for sure.
I would suggest that you pick up a copy of the long trail map as it's quite helpful for any hike on the long trail.
https://www.greenmountainclub.org/products.php?catid=3
http://www.longtrailhiking.info/ also has good info with maps of towns and what services they can supply.
Let me know if you have any other specific questions.
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