when they surrendered in 1945 did the high ups in the Japanese government know which of them selves the Americans would and would not charge with war crimes?

by grapp
JiangZiya

No. The "war clique" of Army Minister Anami Korechika inside the "Supreme Council for the Direction of the War" had been attempting for months to negotiate an armistice through the Soviet Union. Among these conditions were Japan retaining Sakhalin, the Ryukyus, and some other islands, and maintaining jurisdiction to prosecute its own war criminals. Although the Nuremberg trials were not held yet, Hermann Göering and other top officials had been arrested by the Allies, sending a pretty clear message to the Supreme Council that they would likely meet the same fate if they agreed to an unconditional surrender. While preserving the kokutai, the "Emperor system" national polity, was nominally the Council's top priority, it's safe to assume some of them had their own fate in mind as well.

Part 6 of the Potsdam Declaration stated "There must be eliminated for all time the authority and influence of those who have deceived and misled the people of Japan into embarking on world conquest, for we insist that a new order of peace, security and justice will be impossible until irresponsible militarism is driven from the world." Part 10 stated "We do not intend that the Japanese shall be enslaved as a race or destroyed as a nation, but stern justice shall be meted out to all war criminals, including those who have visited cruelties upon our prisoners. The Japanese Government shall remove all obstacles to the revival and strengthening of democratic tendencies among the Japanese people. Freedom of speech, of religion, and of thought, as well as respect for the fundamental human rights shall be established." The wording shows that the decision on which Japanese leaders "deceived and misled the people of Japan" was going to be decided later. The Allies themselves had very little knowledge of the inner workings of Japanese militarism, from Ishiwara Kanji onward, and would have to investigate first.

Not even Hirohito's fate was decided by the Allies until later. One of the key decisions by SCAP (Supreme Commander Allied Powers) Douglas MacArthur and GHQ (General Headquarters) in the early occupation was to largely absolve Hirohito of guilt and promote the narrative of Marquis Kido Koichi and others that he had been duped by the military and held no real power.

This would influence the IMTFE, "International Military Tribunal for the Far East," a sort of low-rent Nuremberg, also known as the "Tokyo Trials." Instead of, say, Supreme Court Justice Robert Jackson at Nuremberg, the Allies had Joseph "the Key" Keenan, pretty much a corrupt drunk whose own nickname suggested he was "the key" to success in a local patronage system. The trials were pretty farcical victor's justice, as Indian justice Radhabinod Pal repeatedly pointed out. The propagandist Shūmei Ōkawa, for example, was thrown out for bonking Tojo Hideki on the head and yelling "This is act one of the comedy!", for "insanity" reminiscent of Vincent "The Chin" Gigante.

It wasn't all clemency for the Japanese, however. Yamashita Tomoyuki, a skilled general nicknamed "The Tiger of Malaya," was tried and convicted in Manila for his troops' atrocities against civilians. Yamashita actually tried, and failed, to stop his troops. This became as the "Yamashita standard," or "command responsibility," and was used against Ernest Medina after the "My Lai Massacre," though he was found not guilty.

TL:DR: "No."

Some of the more popular books on this are John Dower's Embracing Defeat: Japan in the Wake of World War II, Saburo Ienaga's Pacific War, 1931-1945, Timothy Maga's Judgment at Tokyo: The Japanese War Crimes Trials and Hasegawa Tsuyoshi's Racing the Enemy: Stalin, Truman, and the Surrender of Japan.