A good place to buy bento boxes in Tokyo Station IMO:
http://www.timeout.jp/en/tokyo/venue/23174
If you have a lot of luggage - you might want to ship your luggage to your next destination on one or more legs of your trip. It's something that's very common in Japan (trains don't have tons of room for luggage). Costs about $25/bag IIRC.
If you use the JR pass from Narita to Tokyo on the Narita Express - I suspect the "clock" on the pass will start to run. Whether or not that's the case - you might consider taking the limo bus into town (my husband and I have taken the Narita Express back to Narita - but we were so dead on our feet on arrival that I don't think we could have handled it). Also - if you decide not to get a rail pass - your hotel concierge can buy you individual train tickets a few days in advance (assuming you won't be traveling on a major holiday or the like). And - if you do get a rail pass - your hotel concierge can make reservations for you.
We liked Osaka for a few reasons. First - there are 2 food regions in Japan where tons of people live and where there are tons of restaurants - Kanto (Tokyo area) and Kansai (Osaka/Kyoto/etc.). (Note that there are other food regions as well -
http://www.jnto.go.jp/eng/attraction.../jfood_07.html). We wanted to try some of each.
BTW - here's a good English guide to dining in several cities in Japan:
http://www.bento.com/
We also liked some of the Osaka attractions - like the aquarium and the Cherry Blossom and flower festival that were going on there during our trip (don't know if anything special will be going on in Osaka in August) . OTOH - I don't think you've mentioned Kyoto. If I had to choose between Osaka and Kyoto (I didn't) - I'd definitely pick Kyoto.
One thing to consider is all of these cities are really hot in the summer. If you're getting a rail pass - you might consider spending a few days in a cooler part of the country. If at all interested - I'm sure people here can give you some good ideas.
I think everyone here is right about the train travel. It is easy. And the system is so efficient it's almost frightening

. The only thing that I recall being somewhat challenging was getting from our Kyoto ---> Tokyo train to the Narita Express train (Tokyo Station is HUGE and can be somewhat confusing). Allow sufficient time to get lost at least once in terms of any connection times.
Finally - my husband and I took the first class Nozomi from Tokyo to Osaka and from Kyoto to Tokyo. We did it because we wanted to - it was within our travel budget - and because we knew it would be our only chance to do it ever. It was worth it for us - like an amusement park ride

. Whether it's worth it for you is your personal decision (I'm sure the other trains/classes of service are all fine). Robyn