we've been a couple of times. JNTO (japan national tourism board, I think) has a nice website and was helpful for us. I was going to also suggest you look into the Japan Rail Pass. This is a pass that you must purchase before entering the country, and basically gets you all over the country, with very few limitations. It is good from the day you enter Japan until the day you leave. Only available to tourists. However, if I understand correctly, you will be on a tour with your folks all except the last portion of the trip? If this is correct and your train transfers are a part of that organized tour, then it may be more cost effective for you to buy your additional tickets out of pocket. You might want to read up on the JR pass (just google it) and figure out if you would save any money by going that way. Also, while the signs are in English in all the major cities, the Kyoto train station is HUGE. Very confusing, with multiple entrances and exits. First time we went we wandered around forever. And the staffer who spoke english at the info desk was gone.
We finally found our way to our train, but it was exhausting. Any advance info you can equip yourself with re-navigating the building would probably help you a lot. It's an amazing country-have a wonderful time!
