Itinerary and Prices on Hyperdia

Hi - our 12 day itinerary (April, 2023) is TOKYO-KYOTO-TAKAYAMA-KANAZAWA-TOKYO. Also - one day trip from TOKYO to KAMAKURA. We have decided to take a car service from TAKAYAMA-KANAZAWA (so we don't have to take bus, etc.), so we will only need tickets for the rest of the trip. There could be one or two more local "side trips". My research on Hyperdia is showing me the following:

JR PASS: $344/$465 (+ $14 for FED-X) = $358/$479
Without Pass (Buying Tickets): TOKYO-KAMAKURA (round trip): $14/person
TOKYO-KYOTO (bullet train): $40.25/$73.29 KANAZAWA - TOKYO (bullet train): $50.23/$94.51

As I add it up, it does not seem like the JR Pass is worth it, as buying the tickets (regular/green) comes out to $129/$207? I am a bit confused at the prices on Hyperdia, because everywhere else I read that the bullet train from TOKYO-KYOTO costs at least $150? Can you help?