I second everything Solus said about tripping in September.

IMHO, the most important thing to keep in mind when planning your trip: the days are shorter - it gets dark earlier so, obviously, you need to get off the water earlier.

As for weather, we've experienced mid-summer temperatures (two years ago) and we've experienced sleet and high winds (last year) so weather is very changeable.

Water levels are usually at their lowest for the year so wet portages are often dry and paddable water often must be portaged.

Most outfitters are still operating but it is definitely a good idea to call ahead and let them know when you'll be arriving.

Have a great trip!