And some more amplification.

The first night, they should plan on arriving in Tokyo in mid-evening. Arriving into NRT at 5:30 pm, add 1 hour +/- for C&I and other arrival procedures, then 1-1/4 hour on the train into the city. DO NOT TAKE A CAB FROM NRT, unless $250.00+ USD is pocket change. A short cab ride from the train station puts them at their first hotel sometime between 7:45-9:00 pm. A hotel near either Tokyo or Shinagawa Station will facilitate the train trip to Kyoto in the morning. An "early start" would be nice but suggest they think it through. Tokyo train stations are absolute zoos during the morning rush. Unless they want to get on a 6:00-6:30 am train, I suggest planning a 10:00 am departure or later for Kyoto. Shinagawa Station is much easier to navigate than Tokyo Station but is further afield and not as easy to get to. Also, Tokyo Station is almost a tourist destination in itself and should be seen at least once. The run down to Kyoto on the shinkansen will take 2-1/4 to 3 hours, depending on which train is used and from which station.

Friday, Saturday and Sunday night at a nice hotel in Kyoto. They will not have time for the whole "Kyoto Experience" but can see quite a bit and even have time for a day trip to Nara, Osaka or Himeji. We can make suggestions to fit their interests. Nara, about a 45 minute train ride away, is even older than Kyoto with some stunning artifacts, temples and the "giant Buddha." Some of the buildings are over 1000 years old. Osaka is a vibrant, exciting modern city that is a shopper's or foodie's paradise. Himeji is a small city that is home to what is aguably the best preserved, most beautiful feudal-era castle in Japan.

Monday, they can still have half a day in Kyoto if desired. Most hotels will hold luggage even after check-out at 11:00 am. Take a noon-ish or afternoon train back to Tokyo, get checked in to the hotel and have the afternoon and evening Monday plus all of Tuesday and half a day on Wednesday to see some of Tokyo before departure.

As for the Rail Pass, I think it will be an economical option in this case. The round trip Tokyo-Kyoto-Tokyo is just about a wash versus paying for the tickets out of pocket. Since the Pass can also be used to cover the cost of the Narita Express in both directions and any local train trips during the stay (ie. Kyoto-Nara, Kyoto-Osaka or Kyoto-Himeji) it would really offer savings. The only thing you lose with the Pass is the option to use the fastest, more frequent Nozomi shinkansens on the run to/from Kyoto. That isn't really much of a problem as the Nozomi only saves about 20 minutes from Tokyo-Kyoto - 2:25 versus 2:45 +/-. If they elect to use the Rail Pass, they must purchase the "exchange order" before traveling to Japan and then exchange it for the actual Pass upon arrival. That will add a few minutes to their arrival process time but is pretty simple and then the Pass can be used to "pay" for that first Narita Express trip into Tokyo after arrival. There is a "green car" (first class) option to the basic Rail Pass for more money. I have never felt the need to pay the extra as the "normal" shinkansen cars are plenty comfortable for me. Lots of info online: http://www.japanrailpass.net/eng/en001.html . I usually purchase the exchange order online but many travel agents who specialize in travel to Asia will sell them.

As for the nuts and bolts of doing all the above - mine and everyone elses - we can offer suggestions when we know a bit more of their actual plans. I encourage them to pick up a good guide book and cherry-pick a list of things they want to see or do. There is far more than can possibly be done in such a short visit.

EDIT: Forgot to ask. What hotel are they already booked into in Tokyo. That will impact advice on travel and other options.

JR