I started traveling to Japan in 1987 and my last trip was in 1993. During that time I took about 20 trips working on monitors, power supplies, printers, keyboards, mice, system software and fonts with companies like Sony, Mitsubishi, Hitachi, Morisawa, Ryobi for Apple and Microsoft. Out of all the travel I spent little time on vacation except for short weekends for trips that lasted more than a week.
Taking the family to Japan I could leverage all those years of travel and plan a trip that would work.
Luckily I was able to use mileage points in January to book 4 round trip coach tickets from Seattle to Haneda airport. Delta shuts down the Haneda flight from Oct until Mar, and restarts the flights on Mar 30. Haneda is so much more convenient for getting into Tokyo with a 20 min train ride into Shinagawa station. We arrived late as our flight delayed and it was after midnight when we got in. A taxi ride was less than $70 which was fine for the our of us.
For hotels people will typically try the Ryokan for a traditional experience. I went for convenience and booked at a range of Starwood Hotels. I could easily book online and modify the reservations. To start I booked hotels to see how the flow would work. Then my daughter talked to one of her friends and she said Miyajima to pet the deer was the highlight. http://visit-miyajima-japan.com/en/
Miyajima is near Hiroshima. So changed the hotel reservations to add Hiroshima. JR Rail Pass was making sense to travel. http://www.japanrailpass.net/en/ looked at options and decided on 7 day pass green car for the four of us. the Green car was worth it for the extra room and being to reserve seats for the four us together and spin the seats so we can face each other. We were in Japan for 10 days, but we only needed the JR Rail pass for the first part. the last days we were in Tokyo.
To get an idea for travel times I used Hyperdia. http://www.hyperdia.com/ This gave me an idea of what we could do. Our list of travel points were Haneda, Tokyo, Hiroshima, Miyajima, Osaka, Kyoto, Nagoya, Tokyo Disneyland, Tokyo, and back to Haneda.
I used Hyperdia regularly to figure out what trains, times, and platforms to go to. After getting the JR Pass in Japan I started booking bullet train reserved tickets between the cities. The hard part is you cannot start booking tickets until you exchange your tickets in Japan. We had to wait for room for 4 green car reserved for a couple of hours in Shinagawa, but it was worth it given the 4 1/2 hours on trains to Hiroshima.
To get Internet access I rented a standard wifi device for $55 for 10 days. http://www.globaladvancedcomm.com/pocketwifi.html The wifi was shared between all us who ran our phones in airplane mode in Japan with wifi on. The family could e-mail, text, snapchat, and even facetime over the wifi device. I spent most of my time looking up travel details.
For food, we tried to find restaurants to go to based on recommendations, but eventually just started wandering around an area and looking at what looked most interesting to try.
What did work out well for planning ahead was contacting the concierge at the Westin Osaka for baseball tickets to a Hanshin Tigers baseball game. It was a the 80th anniversary so it was hat day.