Just pack clothes that you can wear in layers and peel away as the day goes on, lots of t-shirts/sweat shirts. I wore jeans all the time and even wore shorts for 2 afternoons and we were there the first week in Sept. Bring some kind of rain gear, most likely you will see some along the way. Unless you are doing some kind of glacier helicopter tour you'll just need a warm jacket, a warmer one if going on a glacier. Also nice comfortable walking shoes and bring lots of film, its absolutely beautiful.
I recommend layers, thin gloves, a hat or earband, and silk long underwear. We carried cheap ($10-$15) backpacks from Target so we could carry whatever we weren't wearing at the moment, and our water bottles. Don't forget binoculars, one set per person.
I have taken a removable lined nylon jacket for years, no need for a winter jacket. It is unlikely shorts will be worn in Sept, so only bring a pair or 2, layers are the key. I no longer take jeans, too bulky, take forever to dry and get and tend to stay damp. I really like lined and unlined wind pants. Take up very little room, I also always do laundry in Skagway, can be done in a little over an hour with the great propane dryers.