Nozimi on Shinkansen has non-reserved seat so that you do not have to specify the train. Buying Tokyo-Osaka-Kyoto-Tokyo will apply roundtrip discount so will be slightly cheaper than buying Tokyo-Osaka and Osaka-Kyoto-Tokyo separately. Since your trip will be a simple round trip of Tokyo-Osaka, JR Pass will come out slightly more expensive than buying ticket for Tokyo-Osaka round trip. Also, JR Pass will only allow you to ride on Hikari which runs only twice every hour. With purchasing a ticket you can ride on Nozomi which runs every 12 min. Unless it is a major holiday, you will be fine buying Shinkansen ticket a day before. Having reserved seat will ensure that everybody in your party will sit together. Non-reserved seat have a chance of everybody in your party not able to sit togather.

Bento at Shinagawa station, map of Shinagawa station (PDF file), area says "Food Area" has most selection of Ekiben at Shinagawa station. There are Ekiben sold at Shinkansen platform at Shinagawa station also, but this location has most selection. This "Food Area" is after entering the ticket gate to regular trains and before entering the gate for Shinkansen. This is the only thing you need to be aware.

Bento at Tokyo station, map of Tokyo Station, first floor on Central Passage (area surrounded by "6", "8", an "9") you should see the store "Bento Shop" This place sell Ekiben from all over Japan with a lot of selections. This place is always busy when I have been there. Again, Ekiben are sold at Shinkansen platform at Tokyo station also. But this "Bento Shop" has far more selections. This "Bento Shop" is after entering the ticket gate for regular trains, but before entering the ticket gate for Shinkansen.