Planning a trip to Japan... anyone been there?

[TROLL]

Do they really have Skyrines?

Kidding... my friend has lived outside of Osaka for about 4 years, and all of a sudden he's talking about maybe moving back to the US next year. I don't want to regret never getting off my ass to go visit so its go time.
As it turns out, it looks like the best window of opportunity will be mid-September for me, which is a little sooner than I was originally thinking and I'm already feeling the pressure to book a flight and start making some plans.
I need to decide if I should fly to Tokyo then make my way down to Osaka (train is $120 each way), or fly right to Osaka and make my way around from there.

Once upon a time I was a big traveler... before the days of TST I was out of the country as much as I was in it, lots of trains, buses, planes, ferries, and so on... lots of hotels, hostels, and homestays, and lots of awesome adventures... about 30 countries in all I believe. I'm already psyched to get back into it a little although I'm limited by work to only about 2 weeks here. I was in Japan once for a 4-5 day stretch but this trip will be a lot different.

Anyway... has anyone been to Japan? Trying to get this to all materialize pretty soon and it looks like you need to make reservations with hostels 2-3 weeks in advance minimum, as well as trains, and of course the flight over there. I gotta get a move on so if anyone has any wisdom about it please share. I need to decide whats important for me to see and how long to spend in each place, then figure out the logistics. Going to go pick up a Lonely Planet tomorrow and do some reading.

Welp, hope this inspires some good travel convo. I'm psyched just thinking about it