I agree with everything you are saying but as you said, the idea is mainly fun. Nevertheless, I still think that several of the difficulties can be overcome.
First, I always assume that the attack took place in winter in order to negate the naval threat. The other reason being the one you gave: the Soviet Pacific Fleet lay at the bottom of the sea.
Second, numerous teams could have been landed or shipped long before the attack to ease the troops progression.
I agree that Magadan is fairly remote but it's not only linked by road, it is also linked to the Transiberian.
I agree that these forces are cut from industrial centers but, by the time of the attack, most of these are gone anyway.
Stockpiles might not be that old because the soviet always had a tendency to maintain well equipped units in the far east regions. In addition, this has always been the trial area for new equipments. The first units to be equipped with BMP-3 and T-80 were located there.
At last I forgot about one supply line which proved to be very important in past war for Russia (WW2). It is also largely neglected by everyone else: it is the
Northern Sea Route. We talked about it with Jester who ran an interesting campaign around this (saddly I had no time to play it). This was traveled already in the early 1900's and opened by the Russian as early as the 1930's. As a result, every small harbor on the northern soviet coast is designed to support convoys going that way. As a matter of fact, even to these days, Russia remains the only country with the capability to maintain that route open.
http://athropolis.com/arctic-facts/fact-nepass.htm
Even during the cold war, US had no real way to stop that traffic as it had too few icebreakers. The soviets, however, had about 10 nuclear icebreakers and several dozen regular ones. In addition, given the time of the supposed landing, they would not have to fear much from airstrike. With the failure of the NATO attack on Murmansk, this route will remain open and it is doubtful that NATO destroyed these small unimportant fishing ports.