Don't have time to read the whole thread, but has anyone mentioned that you don't have to validate your JR Pass the moment you arrive?

I've arrived in Japan, spent a week or two in Tokyo or Kyoto, and then validated my JR Pass (doable at any major train station) for journeys around the country. Your pass is valid for 7, 14, or 21 days from whenever you validate it, not from your arrival in Japan.

If your hotel is toward the northern end of the Yamanote line, i.e. within a couple of stations of Ueno, you can save money by taking the Keisei Skyliner into Tokyo's Keisei Ueno station. I think it's something like ¥1750 these days.

If you're staying at a hotel that has direct bus service and you're not arriving at rush hour, that can't be beat for convenience.

For convenience (although not money saving) in traveling within Tokyo, get either a Suica or a Pasmo card. These are debit cards that work on all trains (JR and private) and subways in the greater Tokyo and Yokohama area. They allow you to take advantage of whichever mode of transportation is easiest for your particular destination. They're available in increments of ¥1000 and can be replenished at any train or subway station.