When you left Japan you should have got a "departed" stamp next to that 90 day entry stamp. That effectively cancels that landing permission.

You will need to line up in the normal tourist queues and get a new one. As long as you're not doing it immediately after a 6 month stay you'll be fine - some people abuse tourist visas by doing a hop to Seoul and back. You might want to have proof of your onward flight home just in case they ask why you're coming back in such a short space of time.

Only people who entered on visas and have residence cards and have undergone appropriate re-entry exit procedures when they left the country and can use the re-entry line on the way back.