I used these guys on my last trip (based on info I got here on FT):
www.globaladvancedcomm.com They seemed to have the most reasonable prices for unlimited data, and I wasn't making too many actual phone calls so I didn't care about that. You choose your pick-up location (usually a Narita post office) and just pick up the package under your name. When you are ready to return the phone, you just put the case in the prepared envelope and drop it in a mailbox, which you can do at any airport. If you are familiar with iPhone, you need to associate it with an apple account to purchase any apps (I think to download free ones too). Larger apps like Skype require a wifi connection to download.
Long story short, I got exactly what I expected and it was very useful.