Japanese Travel Survival Guide
As an American that's regularly traveled to Japan over the past ten years — in trips ranging from 2 weeks to 7 months — I've accumulated a few observations and tips that have made getting around significantly easier.
Travel Light
I travel with a carry-onable back pack. Anything larger would be obnoxious when negotiating trains/bus stations. Specifically, I travel with an Osprey Porter 46. Even with that, I usually plan my day around dropping it off as quickly as possible (even if it's prior to check-in, hotels will always hold it for you). Large, hard-shell rolling luggage is popular in Japan but since they're probably only taking it straight to the airport or back, the same strategy wouldn't make much sense for touring Japan itself.
If you ever need to ditch your bag before arriving at wherever you're staying, search any major train station for coin lockers large enough to cram it in (coin lockers are typically deceptively deep and spacious). Typically, you insert your bag first (to ensure it fits), then insert coins to engage the lock and release the key. Increasingly, coin lockers are going digital, able to break change or pay with ICOCA/SUICA and alert you to other locker locations with vacancy, often printing a claim receipt with a keycode to unlock your locker with. All coin locker payments are per-use, so once you unlock your bag, you'd need to pay to use it again. If you can't find a bay of coin lockers, try asking a station employee: "コインロッカーはありますか?(coin-row-kah wa ah-ree-mahs ka?)".