I like your plan. Your plan is current 2015 the best From my view.
But Day 4 or 5 reduce 1 day at Nikko put in Hakone will even best.

Ginza are Japan most high class area. All high class restraurant. Extremly expensive.

Shinagawa are one of Major Station for interchange trains.  You also got plan going Kamakura. Shinagawa better option.

Chain restaurants and some can accept suica.

Most ramen shops with vending machines accept Suica, and by saying that most vending machines do. Convenient shops all accept Suica, even some shops like Don Quijote.

Yes, it is just like our Touch N Go, an IC Card. Just tap on the IC reader (you won't get it wrong) and walk past the barrier (for trains and subs). For vending machines, you tap first for the machine to check balance, then with whatever balance for what you can buy, those buttons will it up and you just press what you want.

For buying things in convenience stores or other shops, just let the cashier know you wanted to pay by Suica, they will activate the IC reader and ask you to tap on it to pay.

Generally it saves a lot of hassle for preparing coins especially at vending machines and stores. And if you don't plan on bringing it back as souvenir, just return it and get back your deposit (make sure you spend all of your credits so that only deduct whatever is left as processing, and you still get back your 500yen deposit).

For me since I wanted to bring it back (as I will be going again), I make a MY Suica at the machines with names printed on it.

yes, like touch and go 

1tips for u... watch youtube
https://www.youtube.com/results?search_query=suica
ur prb will solve in 1 go

i notice last time... some of the park might hv their own website
they keep week by week cherry/plum blossom progress
japan-guide oso hv, but not as details as the park website
gud luk

do u really wan to view cherry blossom?
it really depend how far u really willing to go...

cherry blossom bloom by traveling north
if u miss it in osaka, u can goto tokyo
at tokyo u miss it, goto tohoku area
then everything else failed.... u still have hokkaido

if i were u... i will buy the JR Pass... cheap and easiest way to hunt

wow, 10k for 4days? that's alot. Mine was almost 12k for 10days (2pax), includes hotel, JR pass, food and air-ticket 

For train u didnt take tokyo pass?

i love the subway 

Never used the local lines throughout my entire tokyo stay 

3day subway pass for 1500 yen was a steal

FYI, kons

Grammar problem.
I think his Local line means JR Trains or Keihan line

Vending Machine not except CC.
Cash and Coin only

Not down, it is just that their website is outdated. If you using older version of Firefox (way older) it will work LOL.