My wife and I walked the Great Glen Way a few years ago, also in September; it was lovely. I think that might be the best time to go: not hot, no midges, we even had only one morning of rain. Days are still long enough that you won't get caught out. We did it in 6 days (I think); there are some ups and downs, especially above Loch Ness, but nothing anyone in decent shape can't handle. The last day of our walk, from Drumnadrochit to Inverness, was a little long at 18 miles, but there may be options to break that into two days walking.
We used a company--Easyways, I think--to organize the B&B bookings and carry our bags between them (it was nice to walk with just a daypack holding water, lunch, rain gear, and a sweater). This worked well, and we've used similar services elsewhere in the UK since--West Highland Way, the Thames Path--but it would be possible to organize it yourself if you want to save a little money.
This is a great walk, and a nice way to see this part of Scotland. You'll meet interesting folks along the way--locals, and visiting hill walkers, but we didn't run into any other Americans. Have a great time.