Transportation

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 Disney Resort
* 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 ^__^

But probably there are no planes available from Kansai to Tokyo at the day of my travel.

There are lots of planes from Kansai Airport to Tokyo! Among the airlines, I recommend Starflyer, but they don't seem to have an English reservation interface.

So are there other ways to travel from Osaka to Tokyo?

Yes. Here you go:
http://www.japan-guide.com/e/e4006.html

The cheapest option is the overnight bus.

I want to visit many places in Tokyo. But I don't know what best and cheapest transportations I can use to reach them.

Check the following travel guide:
http://www.japan-guide.com/e/e2164.html

From Chofu, take the Keio Line to central Tokyo (about 30 minutes).

Using a Suica prepaid card is the most convenient way to get around:
http://www.japan-guide.com/e/e2359_002.html

Maybe you need this: This is a helpful site to search the fastest and easiest and cheapest way by train and ferry through Japan:

www.hyperdia.com

There you have to select English on the right menu. Just fill in start and end station and click search. you are done :)