Transportations!!

I am now applying for one month VISA to Japan, and the embassy is asking me to write down my detailed schedule during this trip including transportations I will use to get to these places.
My trip is one month long, in Tokyo only, and my hotel is in Chofu, Tobitakyuu.
I have 2 problems regards the transportations. I searched the web to know how train and subway's system work in Japan, but actually I got lost with many options and companies. So I am here asking you kindly for your help.
1st problem is that my plane arrives to Kansai Airport in Osaka. But probably there are no planes available from Kansai to Tokyo at the day of my travel. So are there other ways to travel from Osaka to Tokyo? Shinkansen maybe? Is there other cheaper options?
2nd problem, I want to visit many places in Tokyo. But I don't know what best and cheapest transportations I can use to reach them. Can you please help me if not in all of them, at least some of them? Or at least give me a map for stations used for these places?
As I said, my hotel is in Chofu near Tobitakyuu Station. And here is a list of the places I am planning to visit:

• Akihabara
• Shinjuku Streets
• Tokyo Tower
• Asakusa Route
• Streets of Harajuku and its shrine
• Yoyogi Garden
• Ueno Onshi Park
• Tokyo Midtown
• The National Museum of Modern Art
• Ikebukuro's Sunshine City
• Odaiba
• Shibuya
• Tokyo international anime fair
• Hiwatari-sai (Firewalking Festival)

I will appreciate any help since I have no time at all to search them all by myself..
Thank you in advance ^__^

Use Hyperdia.
HyperDia | Timetable and Route Search in Japan.

You can check the trains from one place to another quite easily.
Many flights between Osaka (Osaka Airport) and Tokyo (Haneda Airport) are available every day.
You can check the flight schedule as well using the above airport names.

Usually, flights are cheaper than using the Shinkansen train, although ride on the Shinkansen is convenient and comfortable. I recommend the Shinkansen, if the price difference is minimal.

Once you get to Tokyo, ask for directions to get to Shinjuku. Shinjuku is the terminal station for the private railway Keio Line that takes you to Tobitakyuu. To be on the safe side, take the "local service (kakueki-teisha)" train. It's slow, but you won't miss the station.

Keio Line will be the only railway line that will take you (via Shinjuku) to places you want to go in Tokyo. After a while, you'll learn to transfer between the express and local-service trains to get you to Shinjuku faster.
Once you're settled at your hotel, get the Keio Line train timetable and train and subway maps for Tokyo. Traveling by train/subway, though complicated for foreigners, is the cheapest way to get around the city.

Use www.hyperdia.com to find transportation times, schedules, and costs.

All you have to do is list the sightseeing places you did for Tokyo. They are not going to check to confirm you went there.

To reach those places you could use any form of public transportation. Just say JR train line and that will suffice.

This will help.
Tokyo Metro Home