I can't help about the paperwork, but the general sentiment is that the "I felt so welcomed and people were so kind to me" part is only on the surface. Tourists are very welcome in tourist places, not so much elsewhere, and don't mistake politeness for kindness. One common theme when at work is that as a "gaijin", if something goes wrong, it is always your fault, even if you speak Japanese perfectly (a must), and even if you have citizenship (note that Japan doesn't allow multiple citizenship).
Racism (xenophobia, actually) is very present, but in a more insidious manner than in the west. It doesn't mean Japan is a bad place to live in, cleanliness and order are real things, and the low crime rate is very appreciable. Politeness is nice too, but it goes together with hypocrisy, so if you value things like consideration, harmony, and agreement, Japan may be for you, but if instead, you value honesty, directness and to confront ideas, maybe not so much.