Actually I suspect that the focus will still be on Germany as in OTL, although there might be limited American operations in the Kuriles and Sakhalin Island to re-open the supply line to the Russian Far East. It honestly wouldn't surprise me if Magadan gets built up as a supply port, although it may not be ice-free all year round (I'm not an expert on historical or present day climate sadly).
Magadan would require an entirely new railroad to be built across over a thousand miles of some of the worst terrain on the planet, followed by building a bridge over the Lena at Yakutsk, followed by another seven hundred miles of new railroad. In wartime.
That's not happening.
As best as I can tell, the ports of Vanino or Komsomolsk-na-Amure are the best options, at least until Vladivostok is usable again, and even those still need a rail line built to them (OTL, much of that line was built from 1944-46 with German and Japanese POWs). Constructing the Baikul-Amur Mainline is going to be absolutely critical, since during the early part of the war the eastern part of the Trans-Siberian is guaranteed to be interdicted by the Japanese (it basically runs right on the Manchurian border).
As for who to focus on first, the reason Japan needs to be taken down is that until their navy and air force have been annihilated, the Japanese can interdict the UASR-USSR supply line from the Home Islands. They can also mount constant attacks on the Kuriles and Sakhalin from Hokkaido. In order to secure those islands, and thus the Sea of Okhotsk, without spending years trying to bomb Japan into submission first, Hokkaido more-or-less has to be invaded. Once you've done that, you might as well secure the whole island, at which point invading Honshu becomes the next logical step.
I doubt Germany will get nuked, indeed it wouldn't surprise me if they collapse around the same time as in OTL. On the other hand, it is hinted in previous updates that Japan is invaded by both the Soviets and the Americans, which could delay the end of the war until the latter half of 1946.
Neither of your assumptions make any sense. This Germany is going to be getting full economic support from Britain and France (and through them their colonial empires) up until 1943-44. And in order for the Germans to turn west and invade France when they're already at war with the Soviet Union, they pretty much have to have forced something resembling an armistice along the Eastern Front; even the OTL Nazis weren't crazy enough to start a second major front until after the first one was (or so they assumed, at least) rendered irrelevant.
Japan, meanwhile, will collapse even faster if it's being invaded by both the Soviets and the US; either because it's being invaded several years earlier, in which case they would have to hold out for three or four years in order to drag the war on for that long, or because it's being invaded under the same conditions as IOTL, in which case mass starvation is going to collapse Japanese society during the winter and spring of 1945-46 if the invading armies don't manage it first.
There is part of me that suspects that Anne Frank will avoid her OTL fate, it is a strange thing to add right at the end unless it hints towards something, I just hope Jello doesn't make it cheap in some way. (I'm sure he won't...)
The Netherlands are being invaded several years later than IOTL, and will be under German occupation for far less time, so chances are that either things haven't gotten quite bad enough to force the Franks into hiding or they'll be liberated before their hiding place gets rumbled.
I have a funny feeling that the motivations behind Kyoto will be the real point of contention ITTL. I suspect that the reason Kyoto is chosen is to facilitate the revolution in Japan, which will obviously cause tensions between the Comintern and Japan, and controversy within both the UASR and the FBU.
That would be a very silly reason to nuke Kyoto, given that it hasn't had any governmental functions (civilian, military or Imperial) since 1868. It would be like nuking Vienna because the Hapsburgs used to live there.
If it's on the targeting list, it's there for the reasons it was IOTL until Stimson had it removed: it's the largest city left that hasn't already been bombed, and probably has some industrial targets on the southern side of the city. Still not a great target, though; too big to wreck more than a small portion of it, not enough military value. And it's not really near enough to any other likely targets to make it a viable secondary target (a la Nagasaki) or to be able to divert to a secondary target if weather interferes (why Kokura didn't get slagged).