[Storebror]

As a matter of fact, the Americans had exactly three nuclear bombs at their disposal, of which one was detonated at the Nevada Test Site (Trinity). They had put billions of dollars into building these three bombs. After the war, it took them quite some time to build new ones because the uranium and plutonium weren't readily available.
(...)
dropping the third of three prototypes left the US with exactly zero A-bombs to threaten anyone.

So, the worst thing that could have happened would have been two nuclear bombs dropped onto Germany.

Not quite.
There were two tracks for the production of nuclear weapons which were established completely different.

The Uranium Enrichment made it's greatest enhancements in winter 44/45 and the track was set up finally in Spring 1945. From that time on, production went continously and was growing. 2 devices have been finished until August 45, and the production went on with an amount suitable for app. 1 device per 1-2 months.

The Plutonium Reactors started mass production in December 44 ("D" Reactor) and February 45 ("F" Reactor).
The production growed rapidly then, from April to May alone, plutonium production increased five-fold.
By the end of August there were three devices available and 2 already detonated (including the one from Nagasaki).

In fact, if war would have continued into year 46, Germany would have faced at least 2 A-Bomb attacks per month.
Regardless how splattered the military production would have been, there wouldn't be any workers left to produce anything in time.

Best regards - Mike