OK, where souls go.

First of all, as you might have guessed, Atsutane is not impressed by Buddhism's reincarnation theory. Nothing like it is mentioned in the Japanese sources, and it cannot, therefore, be true. He sums up his opinion in this Al Franken-like tanka which he credits to Norinaga:

「釈迦といふ　大をそ人の　をそ言に　をそ言そへて　人まどわすも」

The big fat liar named Sakyamuni
layers lie upon lie
leading people awry.

Nor does Atsutane believe that souls go to Yomi. This was and remains a popular belief, since it is where Izanami no Mikoto went after her unfortunate series of accidents involving the birth of a fire kami and being seen in an impure state by Izanami no Mikoto; it is also, Atsutane notes ominously, influenced by continental thinking (Buddhist and traditional Chinese).

But, in Atsutane's reading, it doesn't specifically say in the Kojiki that dead people go to Yomi. So where do they go? I'll spare you the analysis, but eventually Atsutane comes up with a two-tiered system he feels is supported by tradition.

1. If you erected and worshipped at a shrine, sacred pillar, etc., while alive, your spirit goes there. (A lot of kami and emperors did this.)
2. Otherwise, your spirit basically stays in the graveyard where your body was interred.

This, however, raises the awkward issue of why graveyards are so quiet. To get around this, Atsutane proposes a two-layered existence.

We, the living, find ourselves in the utsushiyo (現世) or "real world", where we are ruled over by a lineage of emperors as is only proper. The souls of the dead reside with the kami in the meifu (冥府, "dark administration") a.k.a. the yūmei (幽冥, "secluded darkness").

The two worlds are sort of superimposed on each other. In particular, residents of the meifu can quite easily act in the utsushiyo. ("This was true long ago and is true today, and so although I shall give no examples here I believe that everyone shall agree that it is obvious.") However, it is not given to us in the utsushiyo to see the meifu. After all, Atsutane explains, it is much easier to see into a bright place from a dark one than vice versa. I found this analogy quite eerie and entirely delicious.

And so we come to the end of our story. When we die, we go to be with the gods in a murky world that exists alongside the bright one we live in. If we had the foresight to build a holy place to go after we died, we go there; if not, we hang around our graves. So I guess those cemeteries with a view aren't so foolish after all.

Further reading.