Hi there,
Unfortunately there is no discount that can be applied for your circumstances. If you plan on using the Shinkansen a lot, which it seems you would if you are travelling from Tokyo to Nagasaki especially if you go via Tokaido Shinkansen (Osaka, Kyoto direct), The JR Pass would be a good option. However, please note that the main function of the JR Pass is to provide travel on Shinkansen and local express trains rather than metro and local city transport, so if you plan on utilising a lot of local city transportation I'd suggest picking up a SUICA (or equivalent) prepaid travel card.
Kind regards,
Alexis