Just like the title says, I was wondering how involved FDR was in the development of the Manhattan Project during and after 1942. Further, what presidential or executive powers could he have utilized to take history in a completely different direction (i.e: possibly halting the project entirely, or deciding to have certain project leaders/commanders and scientists removed all together). Thanks so much!
He did a number of things:
He approved the original formation of the Uranium Committee in 1939, an exploratory program that looked into whether atomic bombs were feasible.
He then approved the expansion of this into the S-1 Committee, the construction of pilot plants, and, finally, the handing over of this work to the US Army Corps of Engineers in order to build an actual bomb (the Manhattan Project qua Manhattan Project).
He allowed the project to have unlimited funding, top wartime priority (which allowed it to allocate huge non-monetary resources, such as workforce and scarce materials), and was willing to use his office to negotiate troublesome issues (such as resolving labor disputes and keeping meddling Congressmen out of it). The money, early on, came from discretionary funds that FDR had access to — it was, from the beginning, a "black" budget that was not accountable. Later Congress had to authorize some of the expenditures so half a dozen top Congressmen were "read in" to the secret, to make sure no fuss would be raised.
He received regular updates on the project from the Secretary of War, the Vice President (Wallace, not Truman), as well as from Vannevar Bush and General Groves.
He even inquired into whether the bombs could be used against Germany in late 1944. (They could not, as they were not ready.) This is, to my knowledge, the only time that FDR got involved with the question of how an atomic bomb might actually be used if they were available.
But he did not micromanage it. He used representatives (notably the Secretary of War, Henry Stimson, and his Vice President, Henry Wallace) to keep closer tabs on it. He almost never did anything more than approve what he was asked to approve. The major exception to this generalization, the time when he really went his own way, was when he accepted the Quebec Agreement with Churchill in 1943, which allowed US-UK collaboration on the bomb. This was very much against what his advisors wanted him to do (they thought the UK had nothing to offer them at that point), but Churchill convinced FDR that it was something that ought to be done. FDR's advisors were really quite unhappy with this and didn't always implement it in the full scale that the British thought they were owed.
By the time the bombs were actually ready to be used, FDR had died, so he was never involved, even remotely, in any discussions of actual use of the bombs, other than the aforementioned query about Germany in late 1944. He was not involved in the decision as to who would run things or who would be removed from the project — this was handled by people underneath him.