I was reading Henry Stimson's work, and it is clear to me, despite his arguments and seasonings as explaibed, that the atomic bombing of Japan was a war crime. But what about these two other instances in the title?
it is clear to me ... that the atomic bombing of Japan was a war crime
Regardless of whether or not you think it, for something to a crime, there has to be a law against it. There was no prohibition against aerial bombardment of enemy cities and the practise was widely used by all sides in the conflict.
You can certainly question the morality of bombing cities, but the legality is beyond doubt.
There was an attempt, in the mid 1920's to adapt the Hague conventions to restrict aerial bombardment, however these were never adopted as legally binding by any side.
In fact, it was not until 1977 than Protocol 1 was added to the Geneva Conventions, specifically prohibiting the deliberate and indiscriminate targeting of civilians. And even so, there are qualifications to this prohibition.