Hia,
Hmm - if you're coming in September you probably can't climb Mt. Fuji - the season is very short from end of July through August. Maybe someone else can confirm exactly. You can get some great views of Fuji though from places like Hakone. The best time to see her in all her glory is during the winter months when the air is clearer - once the heat and humidity goes up she tends to hide in a haze - I reckon she's shy
Disneyland comes in 2 parts here - Disneyland and Disneysea - 2 completely different places but they are next door to each other. If you can avoid weekends and national holidays as bot get packed. I queued 2.5 hours last time just for one ride!
Cheers and all the best