Thanks to you all for the info from an earlier inquiry on schedules. Now the question is whether or not to get a JR 14 day pass. When I get schedules and fares from grace.hyperdia and specify an unreserved seat, I get, for example from Tokyo to Nagoya, a fare of 6,090 Y and a “charge” – unreserved seat of 3,980Y for a “Total amount of money” 10,070 Y. If I add fares and charges for all our trips, they total 48,220 Y (more than the 14 day pass @ 45,100 Y).
What is this “charge?” If it’s a reservation charge, do I need one if I’m not traveling in high holiday periods (May 23 – 31).

Also: I understand that the Yamanote line is covered in the JR Rail Pass. Do I simply show a JR Rail Pass or use it to get a ticket? What’s the average cost from say, Shinagawa to Ueno?

Thanks again. Fodorites have made this a lot easier.

The ticket price is fare plus charge. The fare is the basic amount for point a to point b. The charge is for the type of train...faster costs more money. A seat reservation costs around 500 yen on average on top of the fare and the charge. With a JR pass, reservations are free. The Yamanote line is covered...you won't have tickets for the gates, so use the manned ticket gates and show your pass.

It's called a limited express surcharge (or fee). It is not a reservation charge and you have to pay it if you use a limited express train or shinkansen.

Your option is to pay just the base fare of 6090 and take local trains. Depending on how you are routed you would make between three and eight transfers just to get from Tokyo to Nagoya on local trains and it would take you between 6.5 and over 13 hours.

The cost of the surcharge allows you to make that trip in 100 minutes with no change of trains by taking the shinkansen.

Thanks a ton! That solves a major issue since we do want to take the Shinkansen (and we understand not the Nozomi)on the legs of our trip (Tokyo-Takayama-Kanazawa-Kyoto-Narita). Even if we activate our pass on the second or third day of fifteen day trip (with five in Tokyo), it is economically and logistically smarter to buy the pass for our itinerary.
Every country in which we travel seems to have that one thing baffles us at the start. We've got more to do, but with Japan Rail largely resolved, we can move onto other fun stuff.

Your pass could be useful on day 2 for using the JR lines in Tokyo.