Transportation

Railpass gets you anywhere by train. It needs to be purchsed before entering Japan. It is valid also for city lines and JR. It does not apply only to the fastest (most direct) trains. 

Train schedules are spot on (seconds). Traveling speed over 260 km/h. 

Google maps cover public transportation. 

Car drive is extremely slow due to traffic and speed limits (often 50 km/h even out of city). Highway is couple of times more expensive than a train, but fast. 

There is no rule on unsigned cross-roads: no priority/give way to a traffic from the right, so everyone drives slow and reaches consensus.

In most cities is good to rent a bike. Sometimes even hostels offer that.

Almost all traffic/navigation signs are also written in latin.

Maps

Mapy.cz are fine for tourist trails. 

Geographical Survey Institute of Japan (third party app Android/iOs) offer a possibility of a bit detailed topo maps at higher scale. 

Accomodation

Airbnb, HostelWorld and Booking.com have good coverage.

Info points on train stations can guide on accomodation or maps. 

Local info

Great source of local info japan-guide.com

Weekends and hollidays can be busy: hostels and car rentals can be booked. If hollidays are on weekends, it's delayed to Monday. And galeries closed on Monday are closed on Tuesday. 

Phone & Internet

Prepaid data sim is sold only by bmobile (1 GB / 3500 ¥ (360 MB FUP/3 days). Must be activated from a japan phone (ask seller). Econnectjapan.com can send activated to your hotel (order 5 days in advacne). 

Voice/tarif can' be purchsed by foreigners (Skype OK). You can also rent a protable WiFi router (e. g. on airport) if you want to carry it. 

Some European phones might not work with Japan SIM despite not being blocked by an operator. Second-hand phones are cheap though.