I myself have been to Japan before.
- There IS toilet paper in the public bathrooms. Their toilets are actually rather high-tech and well facilitated.
- Trains are definitely the easiest, cheapest, and generally fastest form of transport. The subway lines can be a bit confusing and hard to navigate for foreigners, however.
- There are practically vending machines EVERYWHERE. And they have a wide range of products available from them as well, like what
>>3 said.
- ATMs can be found in practically every 7-11, or any other largish convenience store.
I don't really have any advice on where to go, but I suggest looking up places and brochures online.