Hi there!
It's hard to give you exact trains / routes to travel on because the best route can change depending on the time that you are traveling. Here's are some amazing tool's that you can use for your planing.
For planning and looking up route information I would recommend using Hyperdia.com. It's a great resource that displays all the information about timetables and train types which you would ever need. Also read out blog post on how to plan with Hyperdia.
An other great tool to look up route's and see what is covered by the JR Pass is out interactive map which you can use to look up stations and train lines, it's also very helpful for getting an idea about distances involved.
I hope this helps and good luck!
Daniel