Time schedule will not be completely the same.they usually change time schedule in every March.But last train never drastically change.
You don't need to go back to Tokyo.Because you are heading to Kyoto the 15th.
Please check the location of Tokyo,Takayama,Kyoto.
About hotel
http://takayamaryokan.jp/english/index.htm
Inn in Hida Takayama Hida Takayama Minshuku Cooperative Society.
Be careful of their locations.Takayama has widest area in Japan.
I think you should reserve a room.SO CROWDED on that date.