I made an initial assumption that the fighting takes place around the fall of Berlin, since that's the moment when both Allied and Soviet forces are in full battle mode and barrel-rolling into each other.
In regards to Japan being bombed first, here are the issues I believe the American leadership would think about:
1. Japan may have been mostly bombed out of existence, but it was still fighting and represented a living, breathing meat-grinder to American troops that were vitally needed elsewhere. With the prospect of the atom bomb it could finish off the last intact Japanese cities and bring the Japanese to surrender, leaving one less front to worry about.
2. In contrast, Russia had undergone relatively little bombardment. While its production in the west had been destroyed, its centres in the Urals were still very intact and producing lots. With only 2 bombs to start with, there wouldn't be much of a dent.
3. Also, Russia was a lot further in its atomic bomb project than Japan was, and better-placed to figure out how the bomb worked if it was dropped on their soil. This was the argument against using it on Germany first.
4. The war started by accident, and there wouldn't be the resolve to 'push for victory' like the fight against Germany. There'd always be the stated assumption that what they were looking for was an armistice, not unconditional surrender. If the Americans merely threatened the use of the bomb, rather than used it directly, it would give the impression that the Americans wanted peace and not the destruction of Russia (the latter would simply make the Russians fight harder) but was capable of it if the Russians pushed.
5. If nothing else, it would provide a second (fifth?) front in the east before pushing inside Russia proper, which would be a tricky proposition in any case, bomb or no bomb.
Also, about the supposed first target of Germany, I managed to google this historical source that suggested Japan was always the first target...
[URL="http://www10.antenna.nl/wise/index.html?http://www10.antenna.nl/wise/435/4302.html"]http://www10.antenna.nl/wise/index.html?http://www10.antenna.nl/wise/435/4302.html[/URL]
So there you have it...