Restaurant Suggestions Needed

Hi all,

My soon to be wife and I will be going to Japan for our honeymoon next month. While we have a bunch of things planned, we find ourselves lacking in restaurant ideas/plans. We'll be in Tokyo, Kyoto and Hakone. As of now the only restaurant we have a confirmed reservation for is Sukiyabashi Jiro, which i understand isn't necessarily the best sushi or experience, but should be fun anyway. Other than that, places that somewhat interest us are:
Daily Chiko
Uobei Dogenzaka
One of the restaurants at the fish market

Things i'm looking for suggestions on:
-Ramen
-Kobe Beef
-Tempura (I hear Kondo is pretty good, but i'm not sure we want to shell out that kind of cash for Tempura)
-Tonkatsu
-Robotayaki

We're spending about half our time in Tokyo with the rest of the time split between Kyoto and Hakone with a possible day trip to Nara. We'll also be spending a day at Disney Sea and attending a Swallows game, so anything around those areas would be awesome too. We're not necessarily tied to any budget, if that matters. Thanks for everyone's help!