Late September is my favorite time at Disney. The crowds are minimal at MK, non-existant elsewhere. Prices are low, the heat's still high (we see this as an advantage, some might not). If I might make a few suggestions:
MK on Saturday is the one place and time where the "low crowd September" seems to not be accurate. This is because you get native Floridians on the weekends, and many of those that are in the World want to see Spectromagic and FITS. And you may want to, also. We've taken the tact of going elsewhere on Saturday (Epcot, the always excellent option), then heading over to MK around 6 PM. You may get in a ride or two while folks are eating, but don't count on it. Grab a spot for the parade and hang onto it through FITS.
Suggestion number two: Stay in MK after it closes. This is always fun, but so few people seem to do so in September. I think we had the front of the castle to ourselves with maybe a hundred people. Great photo ops, and the park is just beautiful when you can really look at it.
Suggestion three: Do MK on a Wednseday. It was a ghost town. I have video tape to prove it. We walked on Slash Mountain three straight times, and I mean walked right into a boat without any queueing. Space Mountain had a two car queue. It's just amazing.
Final Suggestion: If you've never done a waterpark, now's the time. We went to TL on a Monday. Never a line for a ride, plenty of room in Castaway Creek, and because it's hotter than heck, you just enjoy being there so.
Enjoy it. You can't lose with September. Even with shorter hours, you get twice as much done, and you relax doing it.
Pat