Hello everyone,
Thank you so much for all your help, I really appreciate it! I have a
very rough itinerary planned right now (I am still waiting to hear from
the travel agency for finalized details, so I am not sure about travel
times). Please feel free to comment! My main problem is the subways.
I studied the maps like mad, and I still don't really understand
them...!

Day 1
arrive in Narita early afternoon. go to Hotel. wander around area of
hotel that evening.

Day 2 Tokyo
AM:
Tour-- We are supposed to cover Tokyo Tower, Imperial Palace Plaza, and
the Asakusa Kannon Temple and end up in the Nakamise Arcade
- I am not sure how large the tour group is going to be. I wish we did
the Tokyo Tower last, then we could skip it. I sort of want to see the
Imperial Palace and Asakusa Kannon Temple. We have the PM free. I was
hoping to somehow get to Ginza from Asakusa. From what I understand, I
can take the subway? Then after Ginza, back to Hotel, which is in the
Roppongi area. Can I take a subway from Ginza to Roppongi? Does this
sound feasible?

Day 3 Tokyo (free day)
AM: would like to go to Ghibli Museum in Minatara. I have to get to
Shinjuku station from Roppongi, I think. On the way back, I think I
might stop by Nakano for anime shopping if time permits or I might have
to skip and move onto Shinjuku or Shibuya or Harujuku in the evening.
B/c I need to do one of those!!! However, this is all depending on
whether I even get the tix to the museum.

(you see I don't have nearly enough time to do all I want! I am torn!)
I am wondering if I should abandon the tour day in Tokyo altogehter as
Bob M. mentioned... would it be horrible not to see Asakusa
Temple/Imperial Palace? I was a history major, but I also love
fashion, cosmetics, and anime...

Day 4 Tokyo/Kyoto- transit
Shinkansen to Kyoto. Don't know which one (Nozomi or Kodama) yet, nor
what time we depart, so it's hard to plan if we can do anything in the
afternoon after getting to the hotel... will probably have the evening
free, thought we'd roam Gion.

At least I understood the map of Kyoto, and the bus routes! I really
hope the sakura open when we are there!

Day 5 Kyoto
AM- tour again (Gold Pavilion, Nijo, Imperial Palace, Handicraft
Centre) the PM is free.
I think I will go on the tour, and since the last thing is the HC, we
can abandon that if we want. We'll probably head to the Kiyomizu
Temple in the afternoon and stay in that area the rest of the day.

Day 6 Kyoto/Tokyo (our flight leaves from Narita, not Osaka-- so we
lose a lot of time in transit!), stay overnight in Tokyo

no plans yet... not sure what we can do with a half day.

we are trying to get a evening Shinkansen, so we have the morning/early
afternoon free in Kyoto. However, I thought maybe we should spend the
last half day in Tokyo... so we should take the morning Shinkansen to
Tokyo, so we can check out whatever we will miss.
Day 7 Tokyo- Depart from Narita at 3:30 pm