hyperdia

is the web site hyperdia use for travel only on jr lines or other rail/subway lines also. any other web sites we can use to find the times between 2 stations?

a site called Jorudan (http://www.jorudan.co.jp/english/). It will give you the fastest way to get to your destination whether it be using JR and/or subway.

we have a jr pass, do we need to make reservations from kyoto to himeji or can we do unreserve? what times train leave in am? how long is trip?

About 1 hr 1/2 to 2 hrs depending which train you take and which day of the week. The fastest one goes non stop and there are frequent trains as Kyoto to Osaka to Kobe and beyond is a busy route used by many commuters.

Hyperdia will give you times for any trains, even air flights in some cases. It gives you times including transit times while waiting for another train.