When I search on HyperDia, It said I can board LTD Exp. to Maibara station then transfer to Hikari Shinkansen to Kyoto. Yes, you can take a Limited Express Shirasagi to Maibara then make a transfer there to Shinkansen.
(A Limited Express Thunderbird does
not run via Maibara Station.)
Do I need to buy 2 separate ticket at Kanazawa station and Maibara Station? I recommend that you, at your first chance to visit a JR ticket office, would show a memo of boarding dates and train rides (which you hope to have in this journey) to an attendant there, so that he/she can arrange adequate tickets for you.
JR passenger railroad network is operated by six JR regional companies, but you can buy available JR regular tickets at any JR ticket office regardless of companies.
A JR reserved-seat ticket for a ride on a Shinkansen or Limited Express train is available from about one month before the boarding date.
You will get issued two types of JR regular tickets: basic-fare ticket + Shinkansen or Limited Express ticket.
A JR basic-fare ticket corresponds to a basic fare.
If you come to Kanazawa Station by JR from another direction, maybe you can buy your JR basic-fare ticket which covers the both sections to and from Kanazawa at a lower price than buying tickets separately.
A JR Shinkansen / Limited Express ticket corresponds to a Shinkansen / Limited Express surcharge, which is misleadingly called "Seat Fee" in HyperDia despite that it is required also when you cannot have a seat.
In a case where you can make a transfer at Maibara Station from non-Shinkansen to Shinkansen within two consecutive days, you are likely to get a 50-percent discount on the Limited Express surcharge regarding your Shirasagi ride.
In Maibara Station, after getting off a Limited Express Shirasagi train, you can pass through a Shinkansen transfer gate (between the non-Shinkansen area and the Shinkansen area) with your basic-fare ticket and Shinkansen ticket.
(A ticket gate machine at a Shinkansen transfer gate can handle the two tickets at once.)
- Map of Maibara Station (in Japanese):
https://www.jr-odekake.net/eki/img/premises/0610147.gif: Limited Express Shirasagi trains from Kanazawa use Track 7 or 8.
: Shinkansen trains for Kyoto use Track 11.
In Kyoto Station, if you hope to get out via Central Ticket Gate, you will first pass through Shinkansen Central Transfer Gate with the two tickets; your Shinkansen ticket will be collected here.
Then, if your basic-fare ticket shows Kyoto as the destination, you can pass through Central Ticket Gate with that ticket, using a gate machine, and the ticket will be collected; if your basic-fare ticket allows you to travel further, you will need to make the ticket processed manually at a manned window for your stopover.
- Map of Kyoto Station of JR:
http://english.jr-central.co.jp/info/station/_img/kyoto_L.jpg
