I am not familiar with the alps in France but I live in the Swiss alps...
What is the wether like in the alps in september?
I agree with Franco: one of the best months to travel in the alps. This year however, it was not that nice all over. The beginning of October was better and now (close to the end of October) we still have nice travel weather. So it might be perfect, but not always
Take the advice of Franco regarding clothing.
What is the smallest gear you would recomend?
I am running 22 (front) to 30 (rear) on a 28" bike. This gives me around 1.6m per revolution. With that gear I am able to cross passes in the Swiss alps with 10% -12% (e.g. Oberalp, St. Gotthard, San Bernardino) with reasonable effort and a system weight of 100 kg (I am 63kg). Sometimes I however would wish to have one or two gears more, so 22 x 32 or 22 x 34 might be easier for me. I then however might loose one or two of the high gears. I like to travel down quite fast so I opt for 8 m or more per revolution in the highest gear.
and anything else you would recomend?
Take your time. Do not hurry too much. If you are not that much used to the hight, you might feel it... 100 miles in the alps with luggage are IMHO quite far. Better calculate with 80 miles or less, so you will not be disappointed if you can't reach the 100 miles per day. With no luggage however, 100 miles might be quite reasonable.