In your case, while you could barely break even on a 7-day pass, as you mentioned, the validity is 7 consecutive days. If you don't like that, it would be better to skip the JR Pass - for Nikko you can use a Nikko Pass, and just get regular tickets the rest of the way. For an open-jaw itinerary like yours, it is often a waste of money to get a JR Pass, and online there is no shortage of fools who keep saying everyone should get one no matter where they are going. You can save a lot of money on a pass if you do a lot of long distance travel, especially by bullet train, but you should always first check to see if you are at least breaking even first. There are often cheaper alternatives like some regional passes or other options.