JR Pass specific line usage

Hi all,

We're going to Japan next week and we'll be travelling by train with the JR Pass. Can someone please tell me which trains I can and cannot take with the pass? I know the obvious Nozomi, Mizuho and Hayabusa Shinkansen are excluded but other than that it's a bit vague.

For example, I'll be going from Kyoto to Beppu. Now Hyperdia gives me the option to use the JR Special Rapid Service for HIMEJI from Kyoto to Shin-Osaka, from there the Shinkansen Sakura 555 to Kokura and finally the Ltd. Exp Sonic 29. Are all these trains available with the JR Pass? Where can I find this information in detail (I also read something about a homeliner, again no idea what that is).

Thanks in advance!

Link from Hyperdia: http://www.hyperdia.com/cgi/en/search.html?dep_node=KYOTO&arv_node=BEPPU&via_node01=&via_node02=&via_node03=&year=2016&month=08&day=01&hour=10&minute=56&search_type=0&search_way=&transtime=undefined&sort=0&max_route=1&faretype=0&airplane=off&ship=off&sprnozomi=off&bus=off&privately=off&lmlimit=null&search_target=route&facility=reserved&sum_target=7