Family trip to Japan

We are 4 adults and one 6 years old girl travelling to Japan, from October 26 (arriving in KIX) to November 12 (leaving by Haneda).
Our schedulle is:-
-5 nights in Osaka;
-2 nights in Hiroshima;
-2 nights in Toba (Ise-Shima);
-2 nights in Matsumoto;
-5 nights in Tokyo.
We are buying one week JR pass before arriving in Japan , but I want to know if it is possible to buy tickets Hiroshima-Toba and Toba-Matsumoto in Osaka (the train for these cities are not operated by JR, isn't it?) or we can buy them only when we are travelling to each place? Another thing:- our one week JR pass validity is enough to reach Tokyo, or we have to purchase another ticket in Matsumoto? Thanks in advance to all people answering and giving suggestions!!!!!

There is a JR line between Toba and Nagoya. You can use this line to access Matsumoto and Hirohima.

Kintetsu Railway is the other company, with access to Nagoya and Osaka. Tickets for this railway can be purchased at their stations.

The time vary between the two options, so you can use hyperdia timetable website to compare times.

Yes, you can get tickets and most of it is covered by the JR pass. Osaka to Toba is not JR, but not terribly expensive (Y2400 I think). For Toba to Nagoya you can use JR - there is a small section of private rail line (Ise Railways) and there is a nominal (I think Y500) to use that section collected on the train.

I did the trip earlier this month - my guests loved Ise and Toba.

Thank you very much "hakata14" and "Japan Custom Tours" for your very useful answers!!! I certainly will follow what you advised me to do!!! Our trip certainly would be marvellous due to your travel tips. Thank you a lot again!!!!!