Actually, just 3 nights in Tokyo - would be very rush coz there are alot of sites to visit.

Yup, the JR Shinkansen is expensive but if you actually go all around and make full use of it, it's not that costly.

Bus would take you HOURS. Since the 17th you would want to go to Osaka dy, why not check out the overnight bus from Tokyo to Osaka? At least u have a place to sleep whilst on the way there. Coz if not mistaken, take bus about 9hrs leh (if not mistaken). Wasted dy since your schedule is so packed.

Are you not going to Disneyland/Disneysea or Sanrio Puroland? You won't regret it.

I actually was in Tokyo for 8 nights the 1st time round, I make full use of my time and actually went EVERYWHERE in tokyo that's worth to visit. 2nd time round, I just hang out and shop and meet friends and I did not once regret the packed schedule that I have when i went there the 1st time.