I'm aware of the horrific fire bombing against Germany, but if they held out and posed a threat by the time nukes were ready did US plan to strike specific cities?
The US did not make concrete plans for the employment of nuclear weapons until around the time that Germany was clearly done for (April-May 1945). So there was no real target planning for that.
We don't know what might have happened if the war had gone on. The situation in Germany was very different than Japan at the end of the war; the US (and Soviet Union) had already done 99% of the work of the invasion of Europe at that point. The mindset was very different.
There is some evidence that FDR was open to the idea of using the bomb against Germany in December 1944, but the bombs weren't ready so it is a moot point.