Pack light, because porters can be hard to find and storage space in hotel rooms may be tiny.
Although there are no strict dress codes for visiting temples and shrines, you will be out of place in immodest outfits. For sightseeing leave sandals and open-toe shoes behind; you'll need sturdy walking shoes for the gravel pathways that surround temples and fill parks. Make sure to bring comfortable clothing to wear in traditional Japanese restaurants, where you may need to sit on tatami-mat floors. Central and southern Japan are hot and humid June to September, so pack cotton clothing. Winter daytime temperatures in northern Japan hover around freezing, so gloves and hats are necessary, and clip-on shoe spikes can be bought locally.
Japanese do not wear shoes in private homes or in any temples or traditional inns. Having shoes you can quickly slip in and out of is a decided advantage.
All lodgings provide a thermos of hot water and bags of green tea in every room. For coffee you can call room service, buy very sweet coffee in a can from a vending machine, or purchase packets of instant coffee at local convenience stores. If you're staying in a Japanese inn, they probably won't have coffee.