A friend of mine is coming mid June and I did some research for him. I have just copy pasted everything I sent him. Hope it helps you in making your decision.
Here's some info on travelling by Shinkansen to Osaka.
Here's sites you can book from
The above sites offer discounted Shinkansen tickets valid only for tourists and bought outside Japan. Some of these also include Hotels.
The site below offers Japan rail passes, I would also suggest you get one of these as you'll most probably be using the trains a lot. Get the one for East Japan coz thats where you'll be most of the time.
On your way back to Tokyo I would suggest you stop in Nagoya for one night And since you like cars and are coming all this way, might as well visit the Toyota Headquarters In Nagoya.
Here's the site and some useful information:
Come back to Tokyo and you can do the following tours:
I would suggest the Mt. Fuji, Hakone trip for a day. They also have Onsen tours but that you can book from here as it might get a little to hectic to do all these in one day.
This site below offers only English speaking guides but does not do any booking for you. Its good for the night life as there is no booking needed just someone to guide you to interesting places.
Once you're back in Tokyo then there's lots to do like...