The thing is, a lot of my reading suggests that the Japanese government was pretty well on the verge of collapse even before the bombings. Yes, the generals attempted a coup rather than surrender, even after the official decision was made, but evidence strongly suggests that, if the offer had been made before the bombing to allow the Japanese to keep their emperor (which was part of the final peace but not permitted by the terms issued before the bombing), the Japanese government would most likely have agreed to surrender before the bombs were dropped.
I would tend to agree with this, the main hang-up during negotiations was the Emperor. It is speculation though because it didn't happen that way.
It's also certainly true that the targets chosen were civilian targets. Deliberately so. They were looking for a target that hadn't really been bombed yet, which left out all the truly military targets.
You are correct here, but the implications are murky. The targets selected
had no previous bombing so that the scientist/military brass could evaluate precisely what damage had been done by the bomb. Since as you note, there were no military targets available that had the undamaged nature, other targets were chosen. But they were chosen
not because they were civilian but that was all that was left.
What's more, there is a strong suggestion that the US government knew that.
Your readings should have included the US had materials to build three weapons. One was used in the initial test, the other two were used on Hiroshima and Nagasaki. This is pure
speculation on my part, but it seems reasonable to me that once you are out the ultimate bomb and no word comes form the Japanese, what to do? Truman "promised" a reign of bombs like of which had never happened before(words to that effect), but no bombs existed and to build more would take months. So what is Truman likely to do? Delete the part concerning the Emperor and see if that would allow a graceful surrender. Truman knew the casualty rates in the recent operations and I can't believe he would have wanted the continuation of the war if a quicker end was available.