Full disclosure: the areas of Idaho I usually hike are north of where you're talking about--most of what I know about the Salmon River Mountains area is from driving through and car camping in the more accessible places. And it's been years since I've done any hiking back east where you're from, and then not too much.
I'd plan on at least one short shakedown trip, so you can see the conditions, rather than just hearing about them. I think you'll find Idaho mountains and forests very different from what you're used to. A *lot* drier. Bigger temperature variations from changing weather and day vs. night. Tree species and density very different. Elevations are low by Colorado Rockies standards, but timber line is also lower.
Re: bears. There's been some talk about grizzly reintroduction (fiercely opposed by the average rural Idahoan), but there doesn't appear to have been grizzlies in that part of Idaho since the 1930s or 1940s. Have you heard differently, from reliable sources? There's plenty of black bears in Idaho, but much less habituated to people (and more shy) that Nat'l Park bears back east. I'd bear bag and take the usual precautions not to surprise a bear, but wouldn't mess with bear canisters, pepper spray or bear bells. Just my opinion of course.
I think September is a fantastic time in western mountains. It's been a weird weather year (big snowpack, wet spring, slow to warm up), but generally you should have pleasantly warm days, cool nights, and low precipitation. Pack cover isn't much good, compared to a pack liner (which is just one of the trash bags you already carry). I'd also nix the rain pants, replace Seattle Sombrero with light sun hat for days and beanie for nights. A light rainshell should be plenty. I wear wool socks everyday, year round. If you replace your GTX boots with something lighter and more breathable, wool socks should be very comfy--not too cold, not too hot.