I'm not familiar with a 90-day landing permission sticker. But, when you left Japan, did you fill out a two-part card with some basic information that they stapled into your passport? When leaving Japan, they collect one part of that card, then when returning, they collect the other half. If you don't have that card in your passport, then I suspect that you will not be able to go through the resident line. However, more knowledgable people here may know more.