What is the wether like in the alps in september?
probably the best cycling weather you can ask for in the Alps: still warm but not hot, and more importantly, without the so frequent afternoon/evening rainshowers of summertime. However be aware that it can get quite chilly quite fast up there. Never ride without rain gear and warm clothes
What is the smallest gear you would recommend?
that depends on your athletic ability and your fitness level; however, travelling so light, it shouldn't be a major problem
and anything else you would recommend?
maybe you can find
this chart useful in planning your route (it's a list of almost all relevant climbs in France)