I would agree that you are trying to cram in too much.

Without getting into too much detail, I see a few easy fixes.

On your first day in Kyoto, you are running clear across the city for one site, Nijo Castle. The HR is right next door to Sanjusangendo and quite near Gion and the Higashiyama area. Leave Nijo-jo for the first thing the next morning, at the start of your crazy, full day. Substitute Sanjusangendo and/or Yasaka-jinja for that arrival afternoon, before seeing Gion in the late afternoon and evening. The popular Kyoto sites get very crowded after about 9 am, when the tour buses arrive. Nijo Castle is one that becomes a mob scene later in the day and is rather compact. I recommend getting there early to beat the buses. See the larger, more spead-out sites later in the day.

Best timing advice is to plan more time at each site than you think. An hour at each is not enough.

For Tokyo, you list the Edo-Tokyo Museum twice and the national Museum and Ueno Park on separate days. The Edo-Tokyo will be the most fun for a youngster and is right next to the sumo stadium where you might want to visit the sumo museum in the basement. It is very small and will only take a few minutes. A walk around the neighborhood MIGHT run across some rikishi (wrestlers) out and about in the community in their distinctive clothing. The E-T Museum is a gas and will take several hours.

The National Museum is inside Ueno Park so plan them together.

Your Rail Pass will not help all that much inside the cities. A prepaid Suica card will be more valuable for getting around Tokyo as it covers subways as well as trains.

I am not so sure that the 7-day Rail Pass is the best choice for your trip since you are really only traveling Tokyo-Kyoto-Tokyo on JR. You might be better off just buying tickets as you go and using the faster, more frequent Nozomi shinkansens. The Conrad has a direct limousine bus connection back to NRT on your departure morning. You will be returning to the airport during the morning rush. I'd avoid the need to navigate JR train stations at that time by letting the bus driver get me there. Depending on your arrival hotel, you could quite likely use the limo-bus for that trip as well, again avoiding the stations during the 5-oclock rush.

Your itinerary has many great sites. It just needs a lot of scheduling work.

I can't help with dinner recommendations. I never make reservations and just walk around until I see something that looks good.

You are arriving just before the usual cherry blossom season, which typically begins around April 1. Hope for an early spring. If you get lucky, both Ueno Park and Hama-rikyu in Tokyo are great places to see them. In Kyoto, Nijo Casle and the Imperial Palace Park are good as is Maruyama Park in Higashiyama.

Your son might enjoy some time to relax and channel flip the TV once in awhile. He won't understand the language but Japanese TV is very colorful and interesting for kids, particularly the animated stuff and commercials. He might also like the occasional stop at McDonald.s, KFC or Mosburger to get away from all that Japanese food. If he is not comfortable with chopsticks, consider bringing a plastic spoon and or fork for him to carry around. An eki-ben on the train might be more enjoyable if he doesn't have to wrestle with rice using chopsticks.