It’s been a while since I went, but we’re planning for a big trip in May 2017, so I can tell you where we’re planning! In any event, it’s great that you’re planning early.
As you know, there’s probably some places that are highly recommended but are next to impossible to get into unless you’re a regular who’s re-booked right after visiting, e.g. Sushi Saito or Mitani. For sushi, Sawada sounds great. I’d also consider Harutaka or Hashiguchi for your second one. It’s good to have a backup in case reservations aren’t. There are a myriad of possibilities with which you could do quite well. I don’t have personal experience to differentiate among the options. Speaking with some sushi chefs though, I’ve come to the understanding that Sawada and Harutaka would both be great options that are still somewhat accessible for a visitor like me.
Tempura: we’re planning on Mikawa Zezankyo and Tempura Uchitsu.
Yakitori: it’s nearly impossible to get into Torishiki. But, Yakitori Shinka, Toriki (more casual), or Ranjatai (more upscale) are much more approachable and should be good options. I’d probably go with Yakitori Shinka (also note that the chef apparently speaks English).
Soba: Edo Soba Hosokawa, for tenzaru soba and some anago options.
Ramen: Rokurinsha for tsukemen. Ganko ramen for shio ramen. I’m sure others have much more in-depth expertise on this.
Re: Kyoto - I don’t know about which kaiseki to visit there but definitely don’t miss Kawabata Douki for wagashi (it’s been there for 16 generations) and Saryouhousen for tea.
Re: Hokkaido - I’ll ask my friend who’s from Hokkaido. I know she worked at a few renowned seafood places there.