Afghanistan is low level conflict for a while. Japan was a modern army hell bent on taking attrition on the invaders.
In Japan its very unlikely to work out anything like Afghanistan. Once the Japan government was defeated, its unlikely you would have seen a popular insurgency in Japan.
And in Japan an island dominated by allied navies such efforts cold not be sustained anyway.
That actually was a serious concern, both to the US and to the Japanese government itself. If the Emperor and the military leaders had been killed, there was no one who could legitimately order the remaining military to surrender. And the Japanese Army was not small at the end of the war (https://www.nationalww2museum.org/war/articles/there-are-no-...). In addition to the military in Japan (900,000 on Kyushu to oppose US landings), there were something like 1,500,000 in China, Burma, and Southeast Asia.
The result could have been "warlord" led militaries seeking to establish their own territories and fighting with others. Not unlike Afghanistan or China in the 1920s and 1930s, or some other failed states around the world.
Newly free from the European theater, I think Stalin wanted to move in. I'm against the nuclear bombings, but I think if it was between reality as it is now and an alternate history where Japan was cut in half like Korea, I'd choose reality as it is now.
In my opinion Stalin had literally zero chance of invading Japan. They didn't have the ships to do it, and the US would certainty not transport them there.
In Japan its very unlikely to work out anything like Afghanistan. Once the Japan government was defeated, its unlikely you would have seen a popular insurgency in Japan.
And in Japan an island dominated by allied navies such efforts cold not be sustained anyway.