Lots of questions Tristan, I'll address those that stand out.
Weather: Over a period of 10 days in Glacier in mid-September means you're fairly likely to get snowed on. The snow isn't too likely to hang around for long, even at higher elevations, but it gets cold. Make sure your footwear and shelter can handle that.
Camping: GNP requires you stay in designated backcountry sites. On your permit, which you'll need to get at the start of the trip, you'll need to specific your whole route, and they'll expect you to stick to it. If you want to wander at will, looking at the Bob Marshall Wilderness south of Glacier would be a better option. That said, mid-September isn't high season, and getting a permit would not be a problem.
Routes: I prefer to plan routes that maximize time above 6000'. That's the virtual treeline in the park, below which is thick pine and spruce forest, above which is more scattered trees, rocks, talus, etc. Hiking up high means better views.
Fishing: Fishing in Glacier is either in large lakes or smaller rivers and streams between the lakes. There's some excellent fishing to be had, and best of all if you fish only in the park you don't need a Montana license. You'll need to brush up on the park regulations, and follow those. September fishing will mean colder water. I only fly fish, but things like wooly buggers tend to get the job done that time of year.
Bear canister: Won't need one. BC campsites either have a metal locker, metal food pole (if above treeline), or designated hanging area. Bring 30' of rope and you'll be set. MT bears aren't nearly as enterprising as CA bears, thankfully. Must be all the trout and berries they eat.