Having headache on Tokyo itinerary

I'll be traveling to Japan in early June. The 21 days itinerary goes like this:

Day 1(Fri)-Arrival at Narita Airport at around 7am. Place luggage at friend's place(Shiki, Saitama), then visit Sensouji and Asakusa area. Visit my Japan colleagues at Izumi Garden Tower, Roppongi at around 5pm. Visit Tokyo Tower.
Day 2(Sat)-Hakone day trip
Day 3(Sun)-Visit Ghibli Museum. Go to Disneyland by 8:30pm to catch fireworks performance outside the entrance :p
Day 4(Mon)-Kamakura day trip
Day 5 to 14-Hakodate, Noboribetsu, Otaru, Asahikawa, Sounkyo, Biei, Bibaushi, Furano.
Day 15-Travel back to Shiki (takes whole day).
Day 16 to 18-Kyoto, Nara (itinerary settled, thanks to everyone who helped! http://www.japan-guide.com/forum/quereadisplay.html?0+73965)
Day 19(Tue)-Shinjuku, Yoyogi, Harajuku, Shibuya
Day 20(Wed)-Imperial Palace (coz close on Mon and Fri, and tour not avail on Sat and Sun), Imperial Garden, Meiji Shrine, Ueno Park (Goodies!!)
Day 21-Take 1pm flight

Limitations:
1) Day 5 to 18 are already fixed (booked accommodations). Itinerary for Day 1 to 4, 19 and 20 are still changeable at I will be staying with my friend at Shiki, Saitama.
2) Will need to visit my colleagues on Day 1 becoz I will bringing them some goodies and it's a Friday (working 5-days week).
3) Need to place luggage at my friend's on Day 1 so that I don't have to drag it with me while going Asakusa and Roppongi.

Here comes my questions... they are somehow interrelated (mostly on Tokyo and its surrounding areas):
1) Pls see if the attractions for Day 1, 19 and 20 should be rearranged. I do not really know where the attractions are so not too sure if I have arranged something on the opposite direction.
2) I would like to fit in Odaiba in one of my days in Tokyo, planning to see the Statue of Liberty and Rainbow Bridge at night. Visiting Fuji Television building would be a plus. Would also like to fit in Ikebukuro. How can I fit these in my itinerary?
3) Is my Day 1 ok? Is there anyway to overcome limitation no. 3?
4) Did I miss out anything interesting in Tokyo?
5) Am not really a keen shopper on fashion stuff, should I go to Shinjuku, Yoyogi, Harajuku, Shibuya just to have a quick look?
5) Since I will be going to Kyoto, will I be visiting too many shrines and temples if I go to Kamakura/Nikko (either of them) and Meiji Shrine in Tokyo?
6) If I don't go to Nikko/Kamakura, what should I do with Day 4?
7) Was initially planning to go to Hakone and see Mt. Fuji from there, but saw in another post mentioning Fuji Five Lakes is better for a clearer view. Is it easy to navigate around by bus at Fuji Five Lakes? If I'm going to Fuji Five Lakes, which pass is better (will be traveling from Shiki)?

Thank you~~

Pls see if the attractions for Day 1, 19 and 20 should be rearranged. I do not really know where the attractions are so not too sure if I have arranged something on the opposite direction.

Everything is on opposite ends of the city, but travel times between them are not too bad thanks to an efficient train and subway network. Still I feel that it might be a little bit too much for the first day, although I realize that you do arrive early in the morning.

I would like to fit in Odaiba in one of my days in Tokyo, planning to see the Statue of Liberty and Rainbow Bridge at night. Visiting Fuji Television building would be a plus. Would also like to fit in Ikebukuro. How can I fit these in my itinerary?

The Ghibli Museum is not taking an entire day. You could "fill up" that day a little bit more. And depending on your pace of travel, you might have additional time on days 19 and 20. But it depends a lot on the individual pace of travel. For people who prefer a slow pace, days 19 and 20 could as well be already too busy as they are right now.

I think for Tokyo it is okay to just have your list of destinations (with closing days) in mind and then pick them flexibly on the day itself according to your mood.

Is there anyway to overcome limitation no. 3?

You could use a luggage delivery service from the airport:
http://www.japan-guide.com/e/e2278.html

Am not really a keen shopper on fashion stuff, should I go to Shinjuku, Yoyogi, Harajuku, Shibuya just to have a quick look?

Yes, these places are worth a look even if you do not like shopping too much. What are you referring to with Yoyogi? The park?

Since I will be going to Kyoto, will I be visiting too many shrines and temples if I go to Kamakura/Nikko (either of them) and Meiji Shrine in Tokyo?

Depends on the person. For a person with an interest in temples and shrines, it would certainly not be too much. But for those to whom every temple and shrine looks more or less the same, it could be too much. For the average person, though, three days of temples in Kyoto and one day in Kamakura will not be too much. And Nikko is different from Kyoto and Kamakura and should not bore you even if you are not too interested in shrines.

If I don't go to Nikko/Kamakura, what should I do with Day 4?

You have the entire country at your disposal.

Was initially planning to go to Hakone and see Mt. Fuji from there, but saw in another post mentioning Fuji Five Lakes is better for a clearer view. Is it easy to navigate around by bus at Fuji Five Lakes?

I would not call it easy. But it is not too difficult, either. It also depends on where you want to go.

If I'm going to Fuji Five Lakes, which pass is better (will be traveling from Shiki)?

Access to the Fuji Five Lakes is explained here:
http://www.japan-guide.com/e/e6905.html

I personally feel that your intinerary is a bit mixed up.

You are going up then down? Via Japan Rail Pass i guess? Would be good that if you can re-sort your intinerary again. Put all the Tokyo together. You might be able to save quite a big amount of $.

A good intinerary would be like

Tokyo-Fly to Osaka, buy 2-3 days day pass, -Fly to Hokkaido-back to Tokyo.

I understand it is too late now and would probably not have been possible for other reasons, but the following basic itinerary would have been most efficient:

Home - (air) - Tokyo - (air) - Hokkaido - (air) - Osaka - (air) - Home

You are going up then down? Via Japan Rail Pass i guess? Would be good that if you can re-sort your intinerary again. Put all the Tokyo together. You might be able to save quite a big amount of $.
Yes, planning to buy the 21-day Japan Rail Pass tomorrow. Have planned to leave the last 3 days in Tokyo to have the flexibility to extend days in other places, and to make sure I don't miss my flight back home... Tsubasa83, is it because I can buy other passes for Tokyo and buy JR Pass with lesser days that could help to save money?

I understand it is too late now and would probably not have been possible for other reasons
Was initially thinking of making full of the JR Pass, but Day 18 is really taking long hours that I start considering flight again now. Actually I have checked the tickets for AirDo, but not sure if I understand its terms and conditions correctly that is holding me back from buying. Pls correct me if I am wrong? http://www.airdo.jp/fare/list/sp28b.html
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Yes, these places are worth a look even if you do not like shopping too much. What are you referring to with Yoyogi? The park?
Yes, the park, since it's on the way between the places I'm going. But it's tentative. Is it just a normal park?

Depends on the person. For a person with an interest in temples and shrines, it would certainly not be too much. But for those to whom every temple and shrine looks more or less the same, it could be too much. For the average person, though, three days of temples in Kyoto and one day in Kamakura will not be too much. And Nikko is different from Kyoto and Kamakura and should not bore you even if you are not too interested in shrines.
I still dunno if I'll be bored with temples and shrine, I think understanding their background will make the visit more meaningful and not just looking at the building :) will probably change Kamakura to Nikko then ^^

Fuji Five Lakes: I would not call it easy. But it is not too difficult, either. It also depends on where you want to go.
Erm... basically go to all five lakes? It doesn't seems like there are other things to visit other than the lakes and their scenaries... anything notable from this website? http://www.mt-fuji.gr.jp/index_en.php?menu=2

For flights I recommend an air pass by JAL or ANA, since Air Do does not fly between Osaka and Hokkaido:
http://www.japan-guide.com/e/e2364.html

What are you referring to with Yoyogi? The park?
Yes, the park, since it's on the way between the places I'm going. But it's tentative. Is it just a normal park?

Yes, it is just a normal park. Very pleasant. But normal:
http://www.japan-guide.com/e/e3034_002.html

Erm... basically go to all five lakes? It doesn't seems like there are other things to visit other than the lakes and their scenaries...

There is quite a lot to see. The current Fujigoko section on japan-guide.com is simply rather weak. For example, there are a lot of public onsen baths around the area, including Fujiyama Onsen and Yurari. There are also quite a few nice walking trails in the surrounding mountains. There is also Fuji Q Highland, a very popular amusement park. And a lot of museums. There are also a few caves, but they are not outstanding. The Iyashi no Sato village near Saiko is quite nice for seeing and shopping local crafts.

Seeing all five lakes is time consuming and not worth it, in my opinion. Kawaguchiko has most of the attractions around it.

"Yes, planning to buy the 21-day Japan Rail Pass tomorrow. Have planned to leave the last 3 days in Tokyo to have the flexibility to extend days in other places, and to make sure I don't miss my flight back home... Tsubasa83, is it because I can buy other passes for Tokyo and buy JR Pass with lesser days that could help to save money?"

There are other passes in Tokyo like JR Day pass (1000 yen per day) or Toei/Tokyo Metro pass (1000 yen per day)

If you plan properly, a 14 days pass might actually be enough, if you leave about 3-7 days for Tokyo. Osaka, if u want, you can take a night bus for about 4000 yen. =)

For Hakone day trip, you can either buy the Hakone day pass or if you are using Shinkansen, see here for more info.

http://www.japan-guide.com/e/e5206.html

There is a cheap air ticket promotion till Jun 30th. (10000 yen per trip)

Call +81-6-7637-8817

It's under a Visit Japan fare, operated by Skynet Asia Airways, SNA.

Ticket is available at SNA airport ticketing counter or ask travel agent who deals with SNA's VISIT Japan fare.

Note: You must have a "Temporary Visitor" stamp on your passport. (Gotten when you enter Japan).

There are other passes in Tokyo like JR Day pass (1000 yen per day) or Toei/Tokyo Metro pass (1000 yen per day)
I didn't manage to find the 1000 yen day pass that you mentioned.
http://www.jnto.go.jp/eng/arrange/attractions/practical/tonai_ticket.h...
http://www.japan-guide.com/e/e2357.html
They have limitations on type of train that can be taken, right? The thought of taking into consideration which type of train is included while traveling makes my head swirls @_@

For Hakone day trip, you can either buy the Hakone day pass or if you are using Shinkansen, see here for more info.
Yes, I'll be getting the Hakone Day Pass from Odawara Station (3900 yen). Anw, still considering whether to change Hakone to Kawaguchiko (sounds more tempting).

There is a cheap air ticket promotion till Jun 30th. (10000 yen per trip)
Thanks for the information! Will check it out and discuss with my friend :]

This should be the correct link.

http://www.japan-guide.com/e/e2017.html

The JR pass is the Tokunai Pass...