DH and I were there last year (2004) during NOJ. (9/9-9/14.) We experienced light crowds. Most rides were walk on, with other waits being no more than 5 minutes. We did not pay to attend NOJ however. The MK closed early on Friday at 6pm I think. We left the MK at 6pm and took the monorail over to the Poly for our PS at O'Hana. After that, we went to PI.
If you are staying onsite, onsite guests were offered reduced admission (maybe $15 per person) for NOJ on Thursday night.
Frances had just left the area and Ivan was looming, so that would account for the very light crowds. However, I also based our itinerary on peak days/EMH hours and scheduled us opposite those. We also didn't get to parks until 10am each morning (this was our anniversary trip, and we wanted to sleep in) and we got to see everything we wanted to see. I think we rode TOT like 10 times, Splash Mountain just as many.
This was our itinerary for that time frame:
Thursday: MGM
Friday: MK, leave MK at 6pm, dinner, and then PI
Saturday: DTD (meeting friends) and EPCOT
Sunday: BB and Epcot
Monday: MGM (am) and MK (late afternoon, we saw "Wishes" that night.)
Good luck and have fun!