Hi there!
For such a trip you'll be looking at a 14 day rail pass which costs ¥45,100. To know if it will make most sense to you, lets take a look at the equivalent costs if you were to buy the tickets outright:
- Tokyo > Shizuoka: ¥6180, (63mins, 180km)
- Shizuoka > Nagoya: ¥6180, (58mins, 185km)
- Nagoya > Kyoto: ¥5440, (37mins, 147km)
- Kyoto > Matsumoto: ¥9680, (187mins, 335km)
- Matsumoto > Tokyo: ¥9850, (142mins, 285km)
TOTAL: ¥37330 for 5 legs
As you can see, individual tickets may be ¥7770 more economical in your case. However, if you included travel to and from the airport (~¥5000), and take into account that all further JR travel will be free, including all the JR lines in Tokyo (here's map of JR lines in Tokyo for reference) and day trips to Nara, Osaka, Himeji and Hiroshima from Kyoto, then you may find that a 14 day Rail Pass is worthwhile.
Please note that for Tsurugashima you'll need to use non-JR lines (for a small fee). Here is a sample itinerary for you of this trip.
You can look up precise train timetables and costs at the Hyperdia travel planning website and learn how to use Hyperdia through our video blog.
Hope this helps!