Airport congestion depends on many different variables; like the season, how many flights are landing around yours, the amount of manpower Immigration is putting out when you arrive, the number of flights that are landing late (or early), how smoothly other passengers are let through (or not), etc. One bonus is that many airlines are using 777s instead of 747s, so there are fewer people per flight.
If you can arrive earlier, then so much the better. You'll probably arrive a red-eyed zombie, so try to keep it easy on your first day. If you want a cheap way to get to Tokyo, look at the 1000 yen bus.
http://accessnarita.jp/en/home/Or a Keisei+Metro Package might also save you some also.
http://www.keisei.co.jp/keisei/tetudou/skyliner/us/special/index.htmlOtherwise a 3 day subway pass is easy to make worthwhile if you are staying in Tokyo and going all over.
http://www.tokyometro.jp/en/ticket/value/travel/index.html#anc03Studying some history is an excellent way to make your trip more meaningful. But you should do as much as you can before your departure - you will probably be active and not feeling like concentrating on reading a bunch of stuff while traveling.
You could certainly fill up a week just in Tokyo with a broad or well defined area of interests, but you'd be terribly amiss if you missed some good day trips while there - especially Kamakura/Enoshima, Nikko and Hakone or the Fuji 5 Lakes. There are regional passes for all.
http://www.japan-guide.com/e/e2357.htmlFor Kyoto, Kokedera is one of the most beautiful (and pricey) places to visit, but March is not the best time to go - you wouldn't see the beautiful emerald green scenery like you're probably picturing until June and later. You also have to make reservations way ahead of time (several weeks or months), and can't pick your own day or time. If you're going to see Arashiyama though, you should not miss the Otagi Nenbutsuji - it's one of the most whimsical places you will see in Japan.
https://www.youtube.com/watch?v=efvtB_5jmjAFor Nara, as said, 4 hours is more than enough for what you mentioned, and in fact it's well worth including some more. The Isuien Garden is the better of the two there
https://www.youtube.com/watch?v=kk-7IoLELiobut also comparatively expensive - you also might visit the Yoshikien Garden next to it which is free for international tourists (just show them your passport).
https://www.youtube.com/watch?v=vFWGuQ5Z0oISeeing the Kofukuji Temple is also very close and worthwhile, and it doesn't take long to see the Kasuga Shrine as well (and it's free).
For Osaka, I recommend seeing both the Osaka Sky Bldg and Abeno Harukas since the views are not at all the same. Some like one over the other (and the Sky Bldg costs less than half) but if the weather is good, both are very enjoyable - and don't miss Dotonbori at night either.
https://www.youtube.com/playlist?list=PL7LcPcmoSg-jkgQdiQlK2bcKCzr2pJQ...You can easily see Himeji Castle (and don't miss the Kokoen Garden next to it) in half a day, and while you can see Koyasan as a day trip it is far better as an overnight stay. Don't skip either though - they are both very memorable.
A Sunday overnight at a love hotel is one of the less busy times - Saturday night is the worst. Try to go early though to increase your chances and selection.
