Shit--I'm sorry I didn't see this earlier.
We did the eVisa, and it makes immigration check an absolute breeze on arrival. I would strongly recommend it. Just from the looks of the line, I suspect it probably saved us an hour on arrival.
On the Metro tickets, on your iPhone, go to "Wallet" and hit the + on the top right corner. Then go to "Transit Card" and scroll down to Japan. You should get any one of Pasmo or Suica or Icoca. It doesn't really matter. Suica is put out by one of the Tokyo metro companies; Pasmo by one in Osaka. But they're both good on any Metro system nationwide.
You fill them up with some $$ on the front end. Then you just tap your phone at the entry and exit of the Metro. That's it--super easy.
One other nice thing is that these IC cards (e.g., Suica and Pasmo) aren't just used at the Metro. Every vending machine takes them. So does 7-11. I think taxis do, too. So you just use your IC card on your iPhone kind like you would a pre-paid Apple Pay account for a lot of stuff.