JR PASS OR SEPERATE TICKETS

HI .We are arriving in TOKYO on oct10 @ 6.00am and travelling direct to Kyoto for 4 nights.We wish to visit Nara and Kobe on seperate days while in Kyoto On the 14th oct we are travelling to Hiroshima for 2 nights with a visit to Myajima island on the second day. On the 16th oct we will be travelling to Gifu for 2 night and on Sat18th we will be travelling back to tokyo for 5 nights.
Would it be easier to buy the 7 day JR rail pass for 7 days which will get us to Gifu and then buy a one way ticket back to Tokyo or just buy the train tickets separately as we travel.
Is it true that you have to pay extra for the NOZOMI TRAIN even if you have the JR RAIL PASS
Thank You
Brett