Hey,
Akihabara is fantastic to walk around for an hour even without checking out the electronics.
Other than that your itinerary seems pretty solid. Are you going to Hakone for Mt. Fuji or for hot springs? Because there are plenty of other (better) places for hot springs.
As for the JR pass - as you were told you need to purchase them outside Japan. Are you sure you need the national pass? Maybe the one for a specific region would do - check that out. There are specific discounted passes for Hakone travel if I remember correctly. Or see if you want a packaged tour to Hakone including accommodation and transportation if you are looking for a bit of luxury.
In my opinion, Kyoto is quite boring after a couple of days unless you are extremely in to temples and shrines and traditional Japanese culture.
Finally, Disneyland? Really? It's a lot of fun, don't get me wrong, but you are missing out on Japan, if your trip is only 9 days and you are spending 2 in Disneyland.
I think you could get a lot of useful information from my blog -
Smart & Cheap Japan Travel and the book that is coming out soon.