JR Pass + places worth to visit

Hi there,
I have things going on in my mind right now,and would love to hear any advice here :)

So we will be traveling to Japan on April 1-16. We have booked a hotel in Kyoto for 3 days only (I know, we should have planned to stay longer), and we will transfer to Tokyo on April 4, stay in Tokyo for the next 12 days. Plan to visit Yokohama for delicious Ramen :D I know it sounds that we will spend a lot of our time in Tokyo (my husband wants us to just enjoy Tokyo areas as much as we can, he's mesmerized by Shibuya, Harajuku, all those famous areas...the idea is to relax, hang out, etc ... not in rush if you know what I mean) but after I made the list of all places that we're going to visit, it turns out that we still have 2 or 3 days left and we are like "I don't know where to go anymore?" :/ :D

(we booked the hotels 1 month ago, and there were not much hotel options left, except the fancy ones. So we had no choice but to book whatever we could get, or we have no place to stay. that is why we didn't think to visit other prefectures, all we had in our mind was, get the ROOMS first) okay, I know that is long story. sorry I didn't mean to confuse anybody.

Now, I'm thinking that we should at least visit one more prefecture:

1. Gifu (Takayama only, we'll save Shirakawago for our next trip next year) is it possible to do a day trip there? or is it gonna be too much? can we still catch the train to go back to Tokyo? I did check Hyperdia, and it seems it's possible???

About JR PASS and IC Cards:

1. Since we are "stuck" in Tokyo, we will just get ourselves 7 Days JR pass (use from day 1-7: Haneda-Kyoto-Tokyo-Yokohama- (Gifu or Nara or Nikko??) ) is it gonna be a good deal?

2. Which IC card is best for us if we have 7 days JR Pass? Pasmo/Suica? we would like to use the Subway/Metro to get to here and there around Tokyo.

Thank you :)