Considering that AFAIK Japan's leadership intended to make a last stand in the home islands, thus warranting the US at least planning Operation Downfall, did they make any moves to retreat from other theaters than the small Pacific islands? If not, why?
Most of the Japanese armed forces were still outside the Japanese home islands in August 1945. The total strength of the armed forces was somewhat over 6 million. The ground forces numbered about 5.5 million, of whom about 2.4 million were in the Japanese home islands (and about 750,000 of them were on Kyushu to meet the expected invasion). About 1 million were in China, and about 1 million were in Korea and Manchuria (about 3/4 of them in Manchuria, where they would be taken into Soviet captivity after the war, and held for many years for forced labour - most were detained after the surrender, and considered by the Japanese to be internees, but called POWs by the Soviets). About another 1 million were to the south (SE Asia, the Pacific, and Formosa/Taiwan (about 170,000)), and about 250,000 to the north (Sakhalin and the Kuriles).
There were two problems with trying to bring these troops home to reinforce the defences against an invasion of Japan. First, China was a major theatre of operations, where the majority of Japan's fighting on land had taken place, and was still the major land theatre. Occupied China was the biggest item Japan had left for bargaining in a negotiated surrender, and on the (unrealistic) basis of a negotiated surrender after stopping an invasion attempt, holding on to China appeared wise. Indeed, staying in China was the reason for expanding the Second Sino-Japanese War to the Pacific War - the raw materials Japan sought (e.g., oil from Indonesia) and the US embargo making that search for raw materials urgent, and occupying Indo-China and invading Burma to cut off supplies to China were all aimed at continuing the war in China. The Kwantung Army in Manchuria had already been stripped of many of its units for the fighting in the Pacific and in China, and Japan feared a possible Soviet invasion, perhaps as early as spring in 1946. Manchuria needed to be defended, and the Kwantung army was in the process of rebuilding for the task (19 of its 25 divisions had been formed in 1945).
The second problem was shipping. By August 1945, the Japanese merchant marine had shrunk to 1/4 of its pre-war size, and was still shrinking:
The first few months of 1945 saw an effective campaign by the Allies to cut shipping between Japan and the mainland and island SE Asia. January to March saw the Japanese merchant fleet shrink by 30%, and most shipping between Japan and its colonies and occupied territories stopped. After March, the target shifted to Japan's coastal shipping, with high losses from air-dropped mines. Due to loss of ships, and attempting to reduce further losses, much of the traffic was carried by small vessels - too small for torpedoes, forcing submarines to surface and destroy them by gun (one submarine even resorted to landing a demolition party to destroy a train, so few were targets at sea).
Post-war repatriation of Japanese civilians and servicemen back to Japan peaked at almost 200,000 per week, with many of them carried by US shipping, and, of course, no threat of attack. Japanese shipping capacity, post-war, for this repatriation was estimated at about 90,000 passenger spaces, which might have been able to move troops from mainland Asia to Japan at about 40,000 per week, without worrying about precautions against attack. At this rate, it takes 25 weeks to move 1 million troops. The actual rate in practice would have been much lower, and given the Allied naval and air presence, losses due to air, submarine, and possibly surface attack would have been large. Effectively, Japan was cut off.
Invasion plans assumed that a large part of Japanese air strength on the mainland would have been moved back to Japan when the invasion took place, but assumed that ground troops would not have been moved in significant numbers.