Yamanote Line JR East Pass

I am planning to buy a 5 days flexi JR east pass as we will be going from Tokyo to Nagano. Before we do that, we are in Tokyo for several days, staying in Shinagawa. I understand with the JR East 5 day pass, we can use the Yamanote line. But will using the Yamanote line count as using up a day on the pass? It isn't clear from the website if the Yamanote line counts. Thanks!

Why wouldn't it count? If you are using the pass, you are using the pass.

If the pass is valid for five days, then you can only use it for five days. If you activate it early to use on the Yamanote Line, you will "lose" day/s on the pass.

Note that the days are calendar days, i.e. if you activate the pass at midday it still expires at midnight on the fifth day.

The Tokyo-Nagano-Tokyo trip will cost Y16000 on the Shinkansen. You will need to do many trips on the Yamanote line and/or other JR lines around Tokyo to make it worth the cost.
Another fairly long trip will make it worthwhile.
Maybe the Chuo line out to Ohtsuki or the Shinkansen to Utsunomiya, then regular JR train to Nikko, or - - - ?