[Cyclamen]

Only ATMs at major banks accept foregin credit cards. Small ATMs, like the ones you find in your local konbini, accept only japanese cards. I had no problem doing transactions from CitiBank (one of the biggest banks in Japan) with both my Visa and my Mastercard.
Pay pal debit cards work on the Visa Electron system, right? Well, with these cards you can withdraw cash from CitiBank's ATMs, but you won't be able to pay in almost every shop. At least, that happened with a non-paypal debit card I tried to use.
I don't know more about paypal accounts, nor about the fees, sorry. Keep in mind that a lot of stores put an addictional 4 or 5% on the total price if you're paying with a credit card.
Registering for a bank account in Japan isn't an easy task, and you're required to have a long-term visa. I suppose you will have just a tourist visa, since you're staying in Japan for 90 days. (It's very difficult to get something in Japan if you don't have a visa. Heck, it's even difficult to get a proper cellphone in Japan if you have the tourist visa, you can get only a prepaid contract!). Definitely don't go through all the pain this process would take.
My advice would be... open a bank account in the US, and get a Visa credit card. It will be accepted worldwide. Have your dad deposit money on your account and withdraw these money in Japan. If you're staying in Tokyo or another big city, you'll have no problems in finding a CitiBank ATM.
Every time you leave the city, bring with you a lot of cash. Small cities don't have ATMs that accept international cards.

edit: apparently Paypal debit cards don't work on the Visa Electron system, but on the Mastercard system. Theoretically speaking, they will work on every ATM that accepts foregin cards.