Tips: check tabelog (Japanese yelp) for restaurant recs. They're real harsh on reviews there -- if a restaurant is rated above 3.5 you know you're in for a good meal, and finding one above 4 is very rare. Many of the "best meals of my life" I talked about were from restaurants rated about 3.8 or so on tabelog (the 4+ ones were too expensive or too hard to book).
If you know some Japanese, calling restaurants to reserve will sometimes let you eat somewhere that you wouldn't have been able to otherwise. Many restaurants in Japan are very small and/or reservation only without an online option, so being able to reserve in Japanese is a huge advantage. I used Skype to get a Japanese number to reserve with
In terms of Japanese language, like the other guy said prioritize your katakana reading ability. It's by far the most useful bang for buck you could get in terms of language ability.
I did a lot of research before I went so there wasn't much that we didn't expect, but one big thing was how gruelling the jet lag is after the 13 hour flight. We definitely didn't schedule enough restful days upon landing, and next time we'll be sure to take it easy when we first arrive. Best of luck planning your trip!