Nope,
. I introduced myself in the language introduction thread and then got distracted... I'll do that right after this post!
I think you make a good point-- I just don't see a Japanese government enforcing as ruthless a quarantine policy against Japanese refugees as Iceland was able to against foreigners. Longer-term, they'd also have to dynamite the tunnel shut to keep out trolls, which they'd be loath to do. And, thematically speaking, having an island of 5 million make it through the apocolypse intact seems not to jive with the SSSS world, somehow. At the very least, preserving a society of that size through year 90, what with famine and social unrest, seems difficult.
What seems much more likely would be the twin islands of Rebun (pop. 3,000) and Rishiri (pop. 5,500) off the northwest coast of Hokkaido, as the new site of Japan proper. These islands together have 8,000 people, not a single large city. They are only connected to Hokkaido by a single ferry line from Rishiri to Otaru- there are no ferries from Rebun directly to Hokkaido. If Denmark could save Bornholm, then these islands, in the infamously hard to traverse Sea of Japan, could make it through.
Sea Beasts I think would not pose much of a problem. The Japanese do have a huge advantage in the Self-Defense Force, which is one of the most advanced militaries in the world (though legally not a military), and is geared fully towards naval defense of islands.
As for Hokkaido itself, it has much of the same advantages as Sweden- cold enough for cleansing, mountainous enough for defense, enough developed technology for both. I imagine that there would be pockets of surviving communities in northern Hokkaido, and, over time, they could probably link up significant chunks of them, making post-apocalypse Japan not unlike Denmark and Sweden put together.
Expect to see even more lucky waving cats, kitty ears, and cat cafés than you already do...
The romantic in me wants to imagine that, after Japan closed its boarders, the former Kingdom of the Rykuyus declared independence and pulled through.
They do have the advantage of
being home to enormous American and JSDF bases-- if the military went along with it, they could seal themselves off from the outside world forever, and would see a revitalization of the Rykuyuan language and religion-- both of which are distinct from Yamamoto Japanese, and neither of which died off fully. Unlike the Yamamoto, I think the Okinawans would be much more willing to believe in spirits and magic, especially since a sizeable portion of them already do. Continuing my analogy here, it would be not unlike
It would be too warm for cleansing, but, aside from Rebun and Rishiki, this seems to be the place (in Japan, at least) with the greatest possibility of never getting the rash sickness in the first place.