Translation:I will go to Japan tomorrow.
In such a case the wa is optional.
I believe there's a slight difference in emphasis. With the wa the sentence is about what happens tomorrow; without it it's about you going to Japan, which happens to be tomorrow. If you were drawing a contrast between tomorrow, and other days when you're not going to Japan, you'd want to use wa.
But at this stage "it's optional" is probably all you need to know.
I'm a bit confused. I learned in Tae Kim's guide that the particle に doesn't cover relative time such as 明日（あした) or 今日（きょう), but that it works with time like naming months or days of the week. What am I missing here? Is it because the emphasis is on the location you're going to, instead of when it is that you're going?
Yep. The に here is for the place 日本. あした doesn't need a particle. Though you could optionally add a は particle as in あしたは日本に行きます. The meaning would change only slightly, putting more emphasis on the fact that you're traveling tomorrow versus emphasizing that you're traveling to Japan.
に and へ both give the direction but に is giving what you need to do in the direction where you going. But へ giving the direction you are going to (V-ing). Ex: 学校へ行きます。（I am going to school) 学校へ本を買いに行きます （I am going to school to buy the book) So に here used for action you do when you went to the direction you want. Yeah. In the Tips they said ni = to (But seems you all misunderstand it)