Japan is obsessed with cleanliness. The good news is this means health hazards are few and far between. You can drink the tap water straight from the tap and food hygiene is tip top - thank god when there's all that raw fish about. Make sure you follow their lead and wash your hands with soap and water when you can.
Like anywhere you can't guarantee there being toilet paper when you reach out to grab it, but make sure you pick up the free samples available at the major train stations like the locals do.
Some Japanese public toilets do not have toilet paper, although there are often vending machines nearby that sell some at token prices. Do as the Japanese do and use the tissue packets handed out free by advertisers at major train stations.
If on the off chance you are struck down with a cold or sickness get yourself a mouth covering, cloth surgical mask. Locals often wear these out on trains and even sometimes at work, depending on what their job is of course.
If you do have to go to hospital on your gap year in Japan - rest assured that the hospitals there are usually equipped with the most cutting edge medical technology. Although if you're out in the sticks, language could be a problem. Your best bet is to stay safe and clean on your gap year in Japan.