I know the region and I have three times crossed from/to Nejime/Yamagawa, but always in car.
So, I tried from curiosity to find the proper buses and connexions, on the
condition of non week day time table, id. on Sundays and national holidays. Unfortunately, there seems to be no direct bus from Shibushi to Nejime port.
Train from JR Nichinan station to JR Shibushi stationDepartures: 07:19 (next train 11:51)
Arrivals : 08:37 ( 13:10)
Bus from Shibushi-eki-ue to KanoyaDepartures from Kanoya-eki-ue: 08:47/09:27/10:30/11:37/12:45
Arrivals at Kanoya: 09:50/10:25/11:30/12:35/13:45
(See Shibushi station location map of Bus stops)
http://www.city.shibushi.lg.jp/docs/2013101000242/files/download2.pdfBus from Kanoya to Nejime or Nejime PortDepartures: Kanoya City Hall 13:54/15:19
Arrivals at Nejime Port
14:37/16:03This part of the route is the very problem. There are only two buses going to Nejime Port. Some convenient buses donft run on Sundays and holidays.
Departures from Nejime port to Yamagawa port are: (Until October 31) (From November to February)
9:00 9:00
11:00 11:00
13:00 13:00
14:00 14:30
15:00 16:30
17:00
In conclusion, I am sorry, but your plan seems to be impossible unless you accept the ferry of 15:00 or 16:30, or unless you use a taxi or hitchhike from Kanoya to Nejime or from Shibushi directly to Nejime.
(The crossing takes about 50 minutes.
The ferry boat crossing gives you a splendid view, I assure you.)