Can I use the Japan Rail Pass for Gran Class?

No. The standard JR Pass only covers the base fare. You must pay the full 'Limited Express' and 'Gran Class' surcharges separately if you want to sit in that cabin.

Is Premium Class on ANA worth it for a 1-hour flight?

It depends on the lounge access. If you are flying out of Haneda or Itami, the lounge access and early boarding make it worth the 50-80 USD premium for the stress reduction alone.

Routing First Class Travel Across Japan

To route first class, focus on booking the 'Gran Class' service on the Shinkansen and JAL or ANA domestic 'Class J' or Premium Class upgrades. You cannot book an international-style 'First Class' seat on domestic trains, so aim for Gran Class on the Tohoku/Hokuriku lines for the most luxurious experience.

Book Gran Class for long-haul trains. Gran Class is available on the Tohoku and Hokuriku Shinkansen lines. Use the Ekinet (JR East) website to reserve seats at least 30 days in advance. Select 'Gran Class' in the class selection menu to receive lounge access at major stations like Tokyo or Sendai.
Upgrade to Class J or Premium Class for domestic flights. For JAL, look for 'Class J' upgrades (1,000 JPY at the airport). For ANA, choose 'Premium Class' during online booking. Premium Class includes lounge access, full meals, and wider seating, effectively acting as domestic First Class.
Prioritize routes with Green Car if Gran Class is unavailable. If your destination isn't served by Gran Class, book 'Green Car' seats. These are the standard business-class equivalent on Shinkansen and offer 2x2 seating, footrests, and significantly more quiet space than standard cars.
Use a specialized booking agent for complex multi-leg journeys. If you are chaining multiple trains across different JR regions, use a travel agent or the SmartEX app. It allows you to link your IC card (like Suica) to your Shinkansen booking, enabling touch-and-go entry without physical tickets.

Can I use the Japan Rail Pass for Gran Class?: No. The standard JR Pass only covers the base fare. You must pay the full 'Limited Express' and 'Gran Class' surcharges separately if you want to sit in that cabin.
Is Premium Class on ANA worth it for a 1-hour flight?: It depends on the lounge access. If you are flying out of Haneda or Itami, the lounge access and early boarding make it worth the 50-80 USD premium for the stress reduction alone.