Hopefully this topic has not been covered before. We are still planning for our summer trip to Japan and getting more and more anxious and excited at the same time.

We will be in Japan for 12 days (Tokyo, Kyoto, Osaka) and are confused about metro tickets in Tokyo.
We have 7 days JR Pass that we will activate for our Kyoto Trip on day 5, moreover we also plan to purchase N'Ex + Suica pass. That way we can use Suica for our first 4 days in Tokyo.

Questions:
1. Since we will be sightseeing a lot in Tokyo from one place to another, it seems that Metro Open Tix (two days that can be purchased discounted for 980 yen at the airport) makes more sense than Suica/Pasmo. However the open ticket does not cover JR and TOEI lines.

Can one get by to popular locations ie: Roppongi, Shinjuku, Shibuya Asakusa, Ginza, Harajuku, Akasaka, Akihabara without using JR or TOEI line?
We suspect we can although it takes longer time and lots of transit?

2. Which station will we arrive in Osaka from Kyoto? Is it Shin Osaka station or Osaka station?

3. For subway in Osaka, if we will only be traveling from Shin Osaka station to Namba station... if we are not mistaken we can use SUICA pass?

Thank you again. Your expertise and advice are greatly appreciated.