Sorry for this not well proofread wall 'o text, I don't have time to condense it. It's based my analysis of the 3 documents you cited, and to the point of analyzing document #49 was written without close notice to all the points you make above.

The #1 point I'd make in response to them, which I touch on below, is that the Foreign Ministry had no power to speak of in the government to affect the needed change in posture. Not all ministries and ministers are created equal, the US traditionally elevated the Secretary of State to the highest level, xeno"phobic" Imperial Japan not at all.

33, MAGIC intercept (diplomatic PURPLE, and I'll note the leadership of Japan didn't trust the Foreign Ministry as of Pearl Harbor....), Foreign Secretary Togo to USSR Ambassador Sato, July 17th, a month after we took Okinawa, things were utterly dire, the US Navy was freely rampaging on the coasts and 3 days earlier had sunk 7 of the 12 railroad ferries that ran between Hokkaido and Honshu, taking out 80% of 1/4 of Japan's coal supply.

WHOA! I wrote the preceding before reading to the end of this document, based on Whirlwind: The Air War Against Japan, 1942-1945 (https://news.ycombinator.com/edit?id=10132884), and this exact set of facts with numbers is discussed in detail at the end.

Anyway, note this language in the message to Sato:

"Please bear particularly in mind, however, that we are not asking the Russians' mediation in anything like unconditional surrender."

40: Wow, Sato ... spoke truth to power, totally burned his relationship with the government back in Japan (the members of which would soon be tried as war criminals, e.g. Togo died in prison), put Togo, subject to assassination, in an untenable position, and Sato's suggestion for immediate action, what we signaled we were willing to do, and which we actually did, surrender with the one condition of retaining the Imperial House, was utterly rejected.

And in part II we see us signaling the all but Imperial House surrender prior to dropping the first bomb. And:

"I am fully aware of the delicate aspects this matter involves at home."

Yep, do the right thing, get assassinated for your trouble. A bit like Germany falling to the Nazi's, Japan was doomed in the 1920s when a culture of acceptable political assassination developed. That plus a constitution that required the Army to form a government (the Navy as well, but for Japan the Navy was survival, the Army a luxury, a very very expensive one in the end).

Also mention of the rail ferry sinkings in Sato's July 20 message to Togo; it really was a big deal.

Side note, the Japanese never had any air or civil defenses to speak of. They really were unprepared. And they're really concerned about food and the fall harvest, something I've heard before. Plans were being draw up to collect acorns....

Sato also realizes that the only path to peace is through the Emperor, only he had the station to get the Army etc. to stand down, and even then it was resisted with murder (https://en.wikipedia.org/wiki/Ky%C5%ABj%C5%8D_incident).

"The Government will surely choose the road..."; yeah, following this message, just barely after 2 cities got nuked, the Soviets invaded Manchuria, and the Emperor intervened at the possible cost of his life.

"We must also recognize that another cause for the evils we have drawn upon ourselves today lies in the fact that even before the Manchurian incident there were those who showed contempt for diplomacy and indifference toward international relations".

I.e. those who rejected this proposal by Sato.

"We should, however, give a fair hearing to the argument that 'if the enemy actually carries out a landing, we will concentrate all our strength on a counter-attack and will thus bring about his disillusionment."

Note, this is a strong argument. Kyushu had been massively reinforced, 9 division or so, enough to prevent a successful amphibious assault, along with 8,000 or so kamikazes, which, under more difficult conditions, a long flight over water, had off Okinawa inflicted the worse causalities in a battle on the US Navy. Something we had no answer to. BTW, we knew they had ... at least 6,000, our estimate turned out to be an underestimate.

Anyway, Sato is wrong here, Operation Olympic, the invasion of Kyushu, as originally planned was dead except in the eyes of MacArthur, who didn't believe the intelligence we were producing. Those who knew about the atomic bomb were planning on using a total of around 15 in the invasions of Kyushu and Honshu, 5-9 in the former. After the 2nd bomb was dropped, there was serious discussion about using the 3rd in another strike against the homeland vs. reserving it for Olympic. See this excellent account about that period: http://www.amazon.com/gp/product/0691128189

Ah, those who didn't know about the bomb? They were planning the details of liberal use of poison gas, this was not a "clean" theater like the one in Europe, this was war to the knife.

And, as I noted above, Sato's proposal was soundly rejected.

I don't think 49 is at all definitive, I'm not sure it's even useful. It was clearly drafted after the fact, it's undated but written after the surrender, and is a brief summary of two consecutive days two days before Hiroshima.

It's usefulness depends on one non-major actor's interpretation of events that I'm not even 100% sure he was a eyewitness of. I'm not even sure what the hell the content of the middle sentences of the first day is about.

What news was Leahy supposed to be holding out on? Neither he nor his Navy were involved in the future atomic bombings besides potential rescue of crews if ditching was required. It was all Army/War Department, and it almost resulted in the effective abolition of the Navy under Truman (see https://en.wikipedia.org/wiki/Revolt_of_the_Admirals).

Anyway, I still see no better alternative to the bombings as soon as we could possibly do them.