Probably not a great help, but I got a prepaid phone from AMPM. It didn't activate when it was supposed to (I probably smudged the form a little), but I went to a Vodafone store in Akihabara and they got it straightened out for me.
Just hit a Vodafone or DoCoMo store and get the plan you want there, you should just need a passport for a prepaid, not sure if there are any other hoops for a subscription.