Sorry, this is breakdown of your fare.

Your travel on JR will be Kyoto – Kanazawa – Tokyo – Narita Airport.

JR fares are consisted from two components. One is base fare (乗車券) and this is calculated by distance travel regardless of type of train you will ride. One rule of this base fare is that you can buy as one through ticket on Kyoto – (Kanazawa) – (Tokyo) – Narita Airport because base fare rule allows unlimited stop over for journey of 100 km or more as long as you do not reverse the direction of travel. For local commuter train rides, distance will be often less than 100 km so you will not be allowed to do stop over.

Kyoto – (Kanazawa) – (Tokyo) – Narita Airport is 754.5 km in distance, means base fare is valid for 5 day. However, your schedule is more than 5 days from departing Kyoto and arriving at Narita Airport. Which means you cannot use one through base fare ticket to travel from Kyoto – (Kanazawa) – (Tokyo) – Narita Airport. Base fare ticket needs to be divided into two segment of Kyoto – (Kanazawa) – Tokyo and Tokyo – Narita Airport.

Then your plan is to ride on Thunderbird express train on Kyoto – Kanazawa, Shinkansen (Bullet train) on Kanazawa – Tokyo, and let say you will take Narita Express on Tokyo – Narita Airport. Each train requires additional Express Train surcharge (特急料金) and here I am assuming you will have reserve seating.

Express Surcharge has transfer discount if you transfer to another express train in same day, but that is not your situation. Hence, you must purchase express Surcharge for individual trip you are taking.

Following is what you will pay if you buy tickets individually:

Kyoto – (Kanazawa) – Tokyo base fare: 9,830 yen
Tokyo - Narita Airport base fare: 1,320 yen

Kyoto – Kanazawa express surcharge: 1,350 yen
Kanazawa – Tokyo Shinkansen express surcharge: 6,580 yen
Tokyo – Narita Airport express surcharge: 1,500 yen

Grand Total: 20,580 yen

Google maps, Hyperdia etc. only consider sum of individual trips and does not follow fare rules of through ticketing, number of days specific ticket is valid, etc. For multi trip on JR have to know how fare and ticket rules work under that specific routing, and often still require looking up charts and calculating fares manually, not by using some websites.