Itineraries
Three itineraries I've built trip after trip. My strategy is always the same: as soon as you land, head straight to Kyoto — do ancient Japan first (Kyoto, Nara, Osaka), then come back up to Tokyo and its day trips. Pick the length and follow the thread.
Day-by-day plan
Valid for all three itineraries — what I've learned in the field.
Japan Rail Pass
Worth it only if you take lots of trains: heading south, coming back up, many long legs. For a classic Tokyo–Kyoto–Osaka it now costs more than the JR Pass — better to buy single tickets locally. Check the legs on specialist sites. ⚠️ It can only be bought from abroad, before you leave.
Internet
Two ways: a data SIM (Airalo, Holafly or similar, activated before you leave) or a Pocket WiFi — the little device you book on Japan Wireless with delivery to your hotel or the airport. Google Maps is essential.
Where to sleep
In Kyoto: very close to the station (ideally south), it's the real hub for buses to the sights. The rooms there are soundproofed, no problem. In Tokyo: Shinjuku/Shibuya are the liveliest, but anywhere near the metro works. Japanese rooms are small: that's the norm.
From the airport
From Narita, the NEX train gets you to Tokyo Station in ~1 hour (bookable online too). From there the Nozomi Shinkansen reaches Kyoto in ~2h15. If you land at Haneda you're already closer to the centre.