help with trains

Hi, I'm using hyperdia for train timetables and etc.. on one of my trips it tells me to take either a Ltd. Express Kitaniki or a Ltd. Express Hamakaze. Does the JR Pass cover either of those trains? I can't seem to find a list anywhere or exactly which lines of trains are covered.
Also, what happens is I get on a non covered train? Can I pay on board the fare difference?

Hi,

Hyperdia is pretty decent as it will outline each ride and how much it will cost. If it asks you to take a train that will cost more, it will include the cost.

An express train basically skips some of the less used train stations, and a limited express skips even more! Express trains are the same cost as a local train, but limited express will usually cost a bit more.

However, don't worry. If you get onto a limited express train a conductor will come by to check your ticket. If you need to pay more, they will ask for it then and there.

If you get a ticket that doesn't cover the cost of the whole trip but take only local or express trains to get to your destination (no conductor) you can pay the difference when you get to your destination. There are usually machines near the exits that do only that.

For smaller stations, you can always talk with the ticket vender. Even if you speak no Japanese, it's simple. You hand them your ticket and wait. They will either wave you through (ie you paid the right amount) or ask for more money. If you are obviously not Japanese, they will often show you the amount owed with a calculator or try and use English. They often do that with me even when I can understand them.

For the Shinkansen, it's best to go the ticket vender ahead of time and get the right ticket, but it's not always necessary.

If you're in doubt, get the cheapest ticket and pay the difference when you arrive at your destination.

It would help if you told us your starting point and destination.

Hi, I'm using hyperdia for train timetables and etc.. on one of my trips it tells me to take either a Ltd. Express Kitaniki or a Ltd. Express Hamakaze. Does the JR Pass cover either of those trains?

I'm assuming you mean the JR Kitakinki and Hamakaze limited express trains in which case, yes they are both covered by the JR Pass.

I can't seem to find a list anywhere or exactly which lines of trains are covered.

Pretty much all JR trains are covered by the pass except the Nozomi Shinkansen and special compartments such as sleeping berths on night trains. More information can be found here:

http://www.japan-guide.com/e/e2361.html

Also, what happens is I get on a non covered train? Can I pay on board the fare difference?

Assuming there are free seats you may be able to pay on board, however what you pay varies by train. For example, if you take the Nozomi by accident you will have to pay the full train fare, not just the difference.

Also, there are some situations where JR trains run on non JR tracks resulting in JR Pass holders having to pay a small supplement fee. A list of affected trains can be found here:

http://www.japan-guide.com/e/e2368.html

you can use Hyperdia to uncheck Private railways: that will leave ONLY JR options: see if that helps.