I can not speak for what may be present in "Downfall". But about 3 divisions certainly fits what I would expect of the Soviets.
Without any reference to specific Soviet plans, but only with the background of having read of several of their other operations crossing large bodies of water, here is how I would expect a Soviet operation to play out:
First 24hrs: Nights are long at this lattitude during October. During nighttime hours 3 or perhaps 4 re-inforced battalions conduct landings at disparate locations. Probably re-inforced with extra artillery (probably 120mm mortars) and AT assets. Perhaps one of the landings is an air drop. (The Soviets lost their taste for this in combat with the Germans in 1943, but appear to have re-gained it in 1945, as there were several air drops in their campaign against the Japanese.) Each landing force moves to establish a perimeter of about 1 Km radius from the landing point, building a hard but hollow shell with only a very small reserve of 1 or 2 platoons in the center (probably combat engineers, who are engaged in improving their landing site when/if not called on for combat).
The Japanese have no experience with Soviet methods in this kind of operation. The first counter-attack they conduct meets a very stiff defense. As the local Japanese commander, you are likely to interpret these as raids rather than full-scale invasions. They are tough fighters, but in positions offering no mutual support. You will probably seek first to contain them so that they don't grow into a larger threat, and so you work to put screening forces around them as you concentrate a sizeable force to counter-attack the Soviet enclaves one-at-a-time. Divide and destroy them in detail -- sounds like a good plan to most professional military men.
Second 24hrs: The battalions that face stiff opposition are given some fire-support by Frontal Aviation units, but are otherwise on their own. The 2 of the battalions that have succeeded in establishing 1km perimeters are re-inforced during the nighttime hours to re-inforced regimental size, and push their perimeters out to 2 or 3km radius. More artillery and air-defense assets are provided to these expanded beachheads, but they are still primarily a stiff crust, with little filling.
The Japanese have probably finished isolating either the airhead or one of the beachheads, and are busy reducing it. Their attempts to probe at the rest of the beachheads find them to be even tougher than the first, and so they will probably seek to concentrate even more resources as they move on to the next target.
Third and fourth 24hrs: The two largest and most successful beachheads again expand their perimeters out to about a 4km radius. The one beachhead which appears to be facing the least resistance will be re-inforced by two divisions during nighttime hours. As the forces concentrate on shore they are carefully camoflaged and remain still and silent during daytime hours. Each unit that lands carries with it all necessary fuel, ammo and food for 3 days. The second "large" beachhead, the one which does NOT have multi division forces gathering within, will actually become the more active in terms of offensive patrolling, vehicle traffic, and radio transmissions.
The Japanese will likely not appreciate the risk. Given how tough the Soviets are in defense, and how slowly they seem to be building up, they will continue with their one-at-a-time isolation and reduction work. Doubtful they will manage to complete the elimination of even 2 of the Soviet enclaves by the 4th day.
Fifth 24hrs: The floodgates are opened. Two divisions break out of the perimeter, one towards the closest other beachhead in a maneuver which envelopes a sizable portion of the local Japanese counter-force, and eventually clears a significant amount of coastline, the other driving multiple spearheads in an "expanding torrent" deep into the Japanese rear-area, rolling up artillery, logistics and HQ units. At least one airfield will be included as an objective in this maneuver. Also now, for the first time, landings (of the 3rd available division, as well as supplies) will take place during daylight hours.
The Japanese are now past the point of effectively defeating the Soviet invasion. Nothing they have on the ground can stop a Soviet mobile advance. Their Army forces do not have sufficient mobility to get in front of and contain the "expanding torrent", and their top-down decision making is confounded by the high pace of operations of the Soviet advance. Where and when they do manage to assemble a meaningful defense prior to the arrival of a Soviet spearhead, the Red Army simply turned the succeeding waves of the advance in another direction, and the Japanese defense is by-passed. If air resources are concentrated against the daylight landings, there will be no support for slowing the advance of the ground forces. But if the further daylight landings are not slowed/stopped, the torrent just grows and grows.
Could the Japanese have stopped a Soviet advance once it started? I doubt it. In China and Korea the model worked against them nearly perfectly. And the Japanese military, while capable of assessing failures and modifying doctrine to some extent, was certainly not fast at doing so.
