My meager two cents worth. We were in Japan a few weeks ago. Tokyo and Kyoto area. We didn't buy passes except for single day train passes because our schedule and trip was mostly seat of the pants. The pass was not always the cheapest, but trying to figure out how much and where to go for each leg was made easier by already having the tickets. But one suggestion I have is to use google maps to check some likely itineraries. It is AMAZINGLY helpful giving you the actual train times, places you need to switch lines, and even the cost of some of the legs. That way you can see if a specific pass will work for the various train lines you will need (I think I read there are 30 in Tokyo). Just put in the station names or even hotels and google did the rest.
Of course you will need a data plan once you are in Japan, and note that you can't buy voice SIM cards as a foreigner, but you can buy data and SMS SIMS in machines at the airport. Have a great trip! We enjoyed it immensely.
Download the Tokyo Subway IOS app (by Tokyo Metro Co). This will give you the fare, transfer info and time taken for any destination in Tokyo.
The app works without a data connection or WIFI.....you can use it in airplane mode on your phone.
Or, you can combine this with pocket WIFI (I use Global Advanced Communications and have had good experiences) and you will navigate like a pro.