I can't speak to most of your questions since I haven't visited your planned area and I'm not much of a fisherman. However, I can absolutely endorse September! I've tripped in July, August and September and the weather is a major reason why I love September. In general you can expect highs in the 60s-70s with lows in the 40s-50s. This can change dramatically though from year to year. Last year I saw snow flurries (non-accumulating) in the 3rd week of September. In short, I've experienced warm enough temps to swim and last year I enjoyed sleeping cozily in long underwear in my mummy bag. My recommendation is to plan as if you will encounter the cold weather, and then watch the Ely forecast in the week ahead to see if you will actually need to bring that gear.

Enjoy the (likely) comfortable days and cool nights with few bugs, and know that if it ends up being colder there are a few of us September trippers that will be roughing it a bit more with you. :)

Rebecca Falls is Canada. If you're doing this on a Q permit with RABCs and all, no problem. If on a BWCA permit, you'll need a day "vehicle" permit for each canoe from Quetico, as well as RABCs and passports. I did my trips through that area on a Q permit.