Routes during a trip

Hi Everyone,

So, i'm planing a 12 day trip next year. here's my break down:

Flying into HND, Tokyo (Akihabara) > Osaka > Kyoto > Tokyo (do 1 last day shopping and whatever) then fly back out to the states.

Since I've never been, i'm trying to use the Hyperdia site to map out the train jumps but i'm just not getting it. Is there a site or app that can map out routes using only JR pass services? I like how Hyperdia gives you the trains schedule and its ID number but i'm not sure of how to limit the search to only JR trains and buses.

Thanks in advance for any info