Specifically I'm interested in would the Emperor and his senior military leaders have knowledge of comfort women, medical experiments, massacres, etc?
And if so what opinion did he/they hold on it?
Follow up: what did the general populace know of and/or think about the atrocities?
I can't comment on the exact extent of their knowledge, but there was a "competition" between two Japanese officers for who would be the first to behead 100 enemies using a sword. The "race" was published in Japanese newspapers, although now there is some doubt about the historicity of such an event actually happening as described in the news papers.
The context of the killings was generally stated to be in the heat of battle, although we know now this is very unlikely, and I'd even take the leap to call it outright impossible.
Upon returning home, one of the two officers had this to say:
Actually, I didn't kill more than four or five people in hand-to hand combat ... We'd face an enemy trench that we'd captured, and when we called out, "Ni, Lai-Lai!" (You, come on!), the Chinese soldiers were so stupid, they'd rush toward us all at once. Then we'd line them up and cut them down, from one end of the line to the other. I was praised for having killed a hundred people, but actually, almost all of them were killed in this way. The two of us did have a contest, but afterward, I was often asked whether it was a big deal, and I said it was no big deal ...
I don't have any sources on whether this was said during the war or after the war. He was executed in 1947.