https://japantravel.navitime.com/en/

Allows you to specify up front what passes you have, worked brilliantly on our honeymoon, especially when figuring out which Shinkansen reservations we needed to make.

As a rule, unless you have a very specific itinerary that involves a ton of travel within a single train company's network, passes in Japan are not worth it. This applies to both local subway passes and the sadly nerfed Japan Rail Pass for bullet trains. Even the Seishun 18 (unlimited travel for ¥2000/day, but local JR trains only) ain't what it used to be since they switched to requiring continuous days.