If you stick with your revised itinerary, here's a few comments (not counting the ones above that still apply):
1. Buffalo. I assume you mean to canoe this also or just hike?
2. After Zion add Bryce
3. After Canyonlands, add Arches and maybe dinasour museum in Vernal (skip the NM unless you want to see the wall of fossils). Being so close to the Wind River Range, it would be a shame not to try a night there. Park at Elkhart Park trailhead and at least take the Pole Creek Trail (very easy but very boring, too) to Photographers Point. You'll be overlooking one of the bucket list backpacking spots in the world.
4. Maybe add Theodore Roosevelt NP - depends on what you're looking for.
5. Isle Royale. I wouldn't go that far out of the way or spend that much ($100+ for ferry shuttle) unless you're planning to spend several days there. Prepare for bugs!

I'd recommend Andrew Skurka's book to learn more about backpacking gear and skills. Good info for a newbie and easy and quick to read. I've heard the Kindle version isn't a good transfer so stick to the hard copy.