Which passes (JR & Regional) is recommended?

Hello Daniel-san,

We will be visiting Japan for the first time in late March this year. Expert advice is needed and greatly appreciated.
Below is our itinerary:

Tokyo - 4 nights (with daytrips to Kamakura/Yokohama & Nikko)
Nagoya- 2 nights (with daytrips to Shirakawa-go & Matsumoto castle)
Kyoto & Osaka - 5 nights (with daytrips to Nara park, Himeji castle, Hikone Castle)
Back to Tokyo - 3 night (1 overnight in Mt. Fuji area)

1. For Tokyo days, should we get passes or IC cards for subway? If so, which ones?
2. We have luggage (240cm), is it easy to obtain seats with big luggage on shinkansen in ordinary cars during Cherry blossom season? Which JR pass do you recommend Ordinary or Green, 7 or 14 days? Is JR pass upgradable?
3. Do you recommend to use takuhaibin for hotel to hotel? Is this one day delivery service from Tokyo to Kyoto?
4. For Kyoto & Osaka days, should we get Regional pass for bus & subway? If so, which ones?
5. Which navigation apps is best besides Google which does not distinguish JR pass routes?
6. Do you think our daytrips schedule is doable?

Thank you in advance!