What do you mean by "take over?" The US did occupy Japan after the war and strongly encouraged the development of a capitalist democratic society. The soviets never "took" Japan, although they did occupy Manchukuo.

As for why the US didn't immediately declare war on the Soviet Union after defeating Germany; I'm not sure there's any sort of detailed historical answer because it would have been pretty much inconceivable. The US had been at war for years, they were occupying part of Germany, they were still fighting Japan, and they had been supporting their Russian allies the whole time. Although it quickly became clear that these two countries would be in a power-struggle, the cold war didn't take hold instantly - there simply wasn't all that much animosity and plenty of war-weariness.

It's probably worth noting that the idea of preemptive war wasn't as prominent an aspect of US policy back then. Even intervention in WWII was pretty unpopular before the Pearl Harbour attack.

Edit: hopefully someone can give a more detailed description of the Cold War's beginnings than I feel comfortable doing.

You're vastly underestimating the size of Soviet forces in Europe and perhaps overestimating the ability of the United States to go and fight the USSR straight after the end of the Second World War. Nuclear technology was not advanced enough either to really allow the US to dominate the Soviets with what they had. There was a theoretical British plan to carry out an attack on the USSR at this time - "Operation Unthinkable" - but whether it was Britain alone or both Britain and the US, a successful invasion of the USSR would've been near impossible.

Think about it this way; What reasoning on earth could persuade the US or even other countries to go to war with the USSR when Japan surrendered? The Soviet's still had at least some sort of reputation as allies in the war, and why would any leader of a democratic allied country tell the electorate that they were going to invade Russia without popular support and undoubtedly at the cost of a great deal of lives and treasure?

I can sort of understand where you've got this idea from, but I think the simplest answer to your initial question is that it would be impossible for the US to realistically carry out such a task successfully, or at the very least highly improbable and not practical. The Battle of Berlin was costly for the Red Army of course, but they were not "easy pickings" by any stretch of the imagination.

I feel like a real important clarification you have to expand on is why you think the U.S. would/should have overnight attacked someone who was at the time an ally in the war against Japan and recently Germany.

My answer may be too short to answer the entire question(s) posed above but I do want to address this part:

It seems to me the Soviets were easy pickings after losing so many soldiers during the siege of Berlin.

The Soviets were by no means easy pickings. They had recently fought and defeated far more Axis troops in Europe than the western Allies confronted. Their armies were much larger than the British and American forces. The quality of Soviet equipment was good, stronger than the west in tanks, but weaker in trucks and aircraft. It's true that the Soviet armies were short of manpower in 1945, but so were the British, and although the Americans were not really short of men as a nation in the same way the Axis, British and Soviets were, they did have some local shortages in the European Theatre.

Aside from the Soviet forces, the territory of the Soviet Union was huge, with poor communications, and would have been as much of a logistical challenge for the Allies to occupy as it had been for the Germans.

Basically, a decision to invade the USSR would have been a bloody slog with victory not assured. (Conversely, the Soviet forces would have also been very overextended in attacking the west.)