2/4 to 15/4/13

I will be visit Japan for 2weeks. i like to see cherry blossoms for this trip. So i plan to visit Kyoto & Tokyo. I depart at Haneda airport.On the second day i will go down to Kyoto for few day visit and back to Tokyo. I had book hotel at Mt.Fuji on 9/4/2013. Possible can finish my visit at Kyoto? I also plan to visit Nagano also, could you please advise me on the schedule for this visit?

Thank you

I assume you also arrive through Haneda.

The hotel reservation on the 9th is not very convenient. Does it have to be on the 9th or can you move it?

If you can move it, I suggest:

Tokyo - Nagano - Kyoto - Mount Fuji - Tokyo

If you visit Mount Fuji towards the very end of your stay, just before leaving Japan, then you have a chance to see Mount Fuji in combination with cherry blossoms.

My flight arrive at night time about 22.30. What's the safety public transport shall I take? Please advice.
Thanks

Assuming you arrive at Haneda your late night transport options are all explained on this page.
http://www.japan-guide.com/e/e2430.html

In general all transport in Japan is considered safe at night time. Japan itself is a relatively safe country.

Enjoy your trip!