I'm a first time Japan traveller, sorry for the basic question!
We're going to Japan for 12 nights - 6 in Tokyo then 4 in Kyoto then 2 back in Tokyo. So, we have a return trip to Kyoto travelling on days 7 and 11. I don't really want the expense of a 14 day rail pass.
Can we choose the start date of a 7 day pass as day 5 of our trip or does it have to start on the day we arrive? Thanks
No. The subways are mostly metropolitan and separate from Japan Rail. But they're generally cheap, about 200 yen or under, depending on where in Tokyo you're going.
There are some commuter trains in Tokyo that are JR. For example, the Yamanote Line is a train the encircles the Tokyo metropolitan area and is a JR train line. The Railpass is usable for it.