16 day stay in Japan

Hello Daniel-San!

The following is my Itinerary 11.11 - 26.11:

Narita airport - Tokyo(3 days)- Nagoya - Nakasendo Trail - Kyoto (3 days) with a side trip to Nara - Miyajima - Fukuoka - Beppu - Fukuoka Airport.
I assume the JR Pass will cover these destinations - but I realized that I could not use it in Kyoto, Fukuoka, on the way to Fukuoka Airport аnd I would use much public transportation like bus, MRT and train.
I'm wondering if it's worth getting a 14-day JR Pass.
I've never traveled to Japan before and I'm overwhelmed by the various transportation and payment options!

Thanks in advance,
Natalia