The helpful website "www.golf-in-japan.com" is a comprehensive guide in English to golf courses in Japan. It features detailed information on reportedly "all" 2,349 courses of eighteen-holes or more in Japan. The site also includes information on about 500 driving and practice ranges in the central Kanto, Chubu and Kansai areas with additional areas continually added. Over the years its members have rated many of the courses they have played providing a reliable all-around guide from an international players perspective.
In addition to ratings (not all courses have been rated), the site provides price ranges to play each course, the number of holes and par, the year it was established, the designer, and the address. When you click on a specific course on their site it will also provide the contact information/phone number to make a reservations, plus an access map.
Another helpful website is "www.air-golf.com/travel/before-you-go/whats-it-golf-japan." Their page on what to know before you start is very useful and well written. They also have a list of the courses in Japan but it looks almost identical to the www.golf-in-japan.com website listing.
Given the total time and distance involved in this itinerary it is suggested that one break up the trip into two parts. The first part including only the Waseda and Kamakura stops, and the second part covering the rest of the stops. If convenient one could do part one, then take a train to Gifu City and rent a car there for the second part of the itinerary.