Amanohasidate

Hi there,

The last part to Amanohasidate as of Fukuchiyama is traveled over privately owned railroad. This means that you will have to pay a separate charge for this part, even with the JR Pass.

In case you travel on the Ltd exp Hashidate:
The first part up to Fukuchiyama will be covered by the JR Pass and a separate charge of 1480 yen will be charged after for a reserved seat or 1380 yen for a non reserved seat. You can simply board the Train at Kyoto station with the JR Pass, the conductor will ask you for a separate fare once you pass Fukuchiyama.

Enjoy the ride!
-Daniel

How much would it be for a green seat?

I could not find the exact (extra) charge for Green seats but they are generally 50% higher.