Oooooo, very exciting! I did that route in 2006. Best experience of my life, even though bad weather messed up a lot of it.
To start, PM me your email and I'll send you an EXCEL file that I made that shows you all the hotel/hut options for each stage of the trip, elevation gain/loss between every single point, as well as elevation maps I made of each day.
Here are some tips as well:
(1) I found it was cheapest to fly into Geneva and then take the "Alpy Bus" to Chamonix.
(2) Do it counterclockwise so that you become friendly with others on the trail (most do the trail counterclockwise).
(3) You absolutely have to stay at Rifigio Elisabetta, Lac Blanc, and Rifigio Bonatti. Make reservations MONTHS ahead of time. Rifigio Bonatti might be the nicest hut in the entire world and I'm not exaggerating.
(4) You can make reservations for many of the huts ahead of time via email, but you have to email your CC info for most. You don't have to make reservations for most places if it is during the week. However, weekend huts can fill up, especially the popular ones.
(5) There is a website that shows information, dates, prices, contact info for every single hut along the way, but I can't seem to find it though.
(6) The best sections are near Lac Blanc in France and the whole Italian section.
(7) Make sure to take the "Aiguille du Midi" while in Chamonix. It's a cable-car to 12,000 feet and views are AMAZING.
(8) Chamonix is an outstanding base camp. It has probably 50 gear shops.
(9) Plan on only 8-11 miles a day and NO more than that. The terrain is hard. It's like hiking 4,000 footers every single day. You'll want time to shop in markets, take lots of pictures, have beer/wine/lunch at many of the huts along the way, etc.
(10) While you are there, and if you have time, either (1) take a few trains and go to Zermatt and hike near the Matterhorn or (2) take some trains and hike near the Dolomites in Italy.
(11) If you go in September, make sure it is the first week. Don't go any later than that because the weather can get really, really nasty and a lot of the huts close after 9/10 or 9/15.
(12) Buy a good map in addition to the Kev Reynolds book. Sometimes he isn't detailed enough, but 90% of the time he is. I can recommend the best map if you want.
(13) Champex is overrated. Don't stay there an extra day.
(14) Build a "rest-day" into the middle of your trip in case you fall behind. For example, it snowed 18 inches in early July when I went and we couldn't get over one of the mountain passes.
(15)Give in and take the cable-cars when you can cheat. They skip portions of the trail that aren't scenic at all (i.e. the first stage if starting from Chamonix).
(16) Be prepared for weather ranging from 25-80 degrees. The weather is insanely varied along this route, and it can drop 25 degrees in about 10 minutes if the weather is unsettled (reminded me of Mt. Washington or Katahdin)
I like your idea of starting in Courmayer, but keep in mind you'll be seeing the absolute best scenery on day 1. It's kind of fun to start in Chamonix and build up to the Italian side....
You guys will love this route...I'm going to do it again in 5-10 years.