Hyperdia is only showing you the all-first class deluxe Meitetsu trains and the Meitetsu-to-JR connections to Nagoya Station. The direct Meitetsu trains go to the Meitetsu-Nagoya station, which is across the street from the JR Nagoya station where you catch the shinkansen. In this case, Hyperdia is not your best choice for finding train schedules. Instead, use the Meitetsu schedule linked from the Centrair site here: http://www.centrair.jp/en/access/ac-...ain/index.html .

There are trains leaving every few minutes - some the regular trains for 850 yen and others the deluxe, all first class for 1200 yen. Just ride whichever you want to Meitetsu-Nagoya and walk across to the JR station for the shinkansen. I am unsure whether the Help counter in the middle of the Access Plaza can exchange a JR Pass voucher but think not. You will probably have to do the exchange after you get to the main JR station in Nagoya, then make your shinkansen reservation after that. When I have done that arrival (UA SFO-NGO) I chose to stay the night in Nagoya and continue on west the next day but I think there would be time to catch a late shinkansen if you don't mind arriving in Kyoto late that evening.

JR