I just came back from a 10 day stay in Japan and visited a lot of the areas you're talking about going to, so hopefully I can pass on a few 'words of wisdom'
1. From Narita, it will take you about an hour to go to Tokyo Station, and about 1.5 hours from Narita to Shinjuku station and will cost you approximately $30 per person each way via JR's N'EX line. There are other methods to get to / from the airport, but the N'EX is not dependent on traffic and it's so much nicer IMHO than any bus could be.
2. What I'd recommend is buying a travel book to figure out what other areas you'd like to go and see first before trying to make any hotel reservations. Try and make one of your destinations as your 'home stop' so at least as you can explore the place as you go to / from the nearest train / subway stations. If you do stay in Shibuya, it should take no more than 15 minutes tops travel time between Shibuya station and Nakano (not counting time getting to the station). And don't worry about finding Nakano Broadway mall - from the tracks of the station at Nakano, you can see it's right outside of the station
3. Rail passes, if you're talking about the JR railpass really isn't worth it unless you start doing extensive out-of-Tokyo travel via Shinkansen / bullet train. If you stay in the Tokyo area only, I'd pass on the railpass. To let you know, my better half and I spent around $6 a day each just on traveling by trains / subways, so it's really inexpensive - I believe the most expensive fare I had was a 210Y fare going one way (about $2 - not bad at all). I believe a 7-day railpass (which is only good for JR trains, which aren't the easiest ways to get around to some of the places in Tokyo, sometimes) is in the $150 range per person. Besides, riding the train/subway is a very good way of using up all those coins you'll be getting as all currency below 1000Y is in coinage
4. For Nakano, depending on how many series you collect from and if they're still popular enough for the stores there to have it, and your own patience level, I'd say spend the better part of the day at Nakano. That way it gives you uber time to browse thru the stores there, and look thru all the cels and whatnot. When I went about a month ago, there were 3 major stores there: Mandarake, another cel dealer I couldn't ID (both of these were on the 4th floor IIRC), and Anime World Star (on the 3rd floor). AWS and the other dealer I couldn't ID were extremely helpful to the 'gaijin' - actually helping me look for the cels, even! I'd suggest bringing along with a printed piece of paper with the Japanese characters for the shows you're going to browse for or if you can't find them, bring a printed picture of the characters - they may know what you're looking for and help you isolate which binders to look thru (especially AWS - they have TONNES of them!).
As for other places, unless you're going to specifically look at a store and shop until your wallet screams 'uncle', I'd say for most other places, a half day would be good to plan for most places. You won't be able to see everything, but you'll get a very good overview of each of the places you'll be able to visit. Just remember most stores and such seem to open at 10AM, so if you're an early riser, I'd suggest relaxing with a cup of coffee or the like before you start your shopping spree / site seeing for the day.
5. cheap ramen shops are very easy to find. A lot of them are 'smart' restaurants - where the menu is actually a ticket machine usually with a pictures of the food and the costs. You just insert your coins into the machine, press the big buttons that corresponds to it, and it spits out a ticket that you give to the person behind the counter and they bring you your food. A lot of these places also have barley tea free of charge at your table or at the counter so no need to buy drinks, either! On average, the price ranges in the Y600 yen area depending on add-ons and whatnot. You could comfortably eat there for under Y1000 per person per meal.
There are also a lot of other eateries that aren't too expensive, either - most of the cheaper establishments will usually have 'plastic food' displays just outside so worse comes to worse, take the waiter / waitress out with you and point at what you want to eat

. The only time it becomes a bit harder is if you have special eating requirements - my girlfriend is a vegetarian, so we had a bit more challenging circumstances but we never went hungry!
Oh, and as a sidenote - don't be afraid to check out the convenience stores in Japan for meals. You can't throw a used chopstick in any direction without hitting one of the many chains of convenience stores. And don't think of it in Western terms - the Japanese stores have
a lot of food there - and relatively cheap too. You can even buy yourself a yakisoba sandwich (which I sadly never tried... maybe next time) or a croquette sandwich (which I did try, and it was pretty good, if not a bid weird). All in all, you won't go hungry in Japan, even on a budget.
For cheaper hotels too - consider going to a business hotel. They are geared for the Japanese business man and are usually rather small in size as compared to budget rooms in the West, but really, how much time are you gonna spend in the room, anyway? Of course, most don't have all the luxuries of a 'standard' hotel, but are you really gonna order room service? Or bellboys? The two business hotels we stayed in were extremely reasonable and quite comfortable - and easy to find under your 10,000 Y limit per nite. My suggestion is to find one that is close to a subway station - the closer the better as by the end of the day, you'll be extremely tired from all the walking you'll be doing (and bring good shoes with you too).
But my best piece of advice - buy your travel books now and study them. don't limit yourself to just the places you've mentioned as you'll kick yourself if someone tells you later "oh, you were there? You should have gone to such-and-such, it was like only 1 stop away from where you were staying and they had...." you get the idea
hope that helps
darlingapple wrote:As I am planning to visit Shibuya as well, can anyone advise me on the travelling time from Ikebukuro to Shibuya? I do not want to be stuck on an hour train ride bearing the weight of my shopping bags.

At the same time, can anyone also advise me on the following:
1) What is the travelling time from Narita Airport to Shibuya?
2) Should I stay in Shibuya, how long will I have to travel to get to Nakano?
3) What (colour if any?) train (affordable and fast?) can I take from Narita Airport to Tokyo and to Shibuya? I read from websites that it will be wise to get an unlimited train pass or something like that if you are planning to take the train on a regular basis for shopping and sightseeing? Is that right?
4) As I am only going to be there for 5 days and I plan to visit only Nakano, Shibuya and Ikebukuro, will there be enough time for me? Or there's time for me to visit a couple more places?
5) Any nice affordable (1,000 yen and below) ramen shops to recommend?
Sorry guys, seems like a lot of questions but I need as much information as possible so that I will not be panicking when I reach there.
Thanks everyone!
