Before I take a stab at answering your question, note that the question itself (and the information you follow it with) isn't totally logical and contains some inherent biases... and makes answering your question with anything short of literal histories of Japan rather difficult.

How did Imperial Japan change from being as enemy of the Allies during WW2 to one of the most technologically advanced nations in the world?

There's no logical connection between Japan being an enemy of the Allies and not having technological advancement. While it's probably more true than not that the Allies had more technological innovation than otherwise (the Enigma Machine and Radar in the UK, synthetic nylon and the Manhattan Project in the US, and we can even dabble in Germany if we're looking at Western Nations in general) there's nothing inherent about being an enemy of the Allies that makes Japan technologically backwards versus today where things are different.

I'm guessing, but I feel like I'm taking a leap, that you're asking about how Japan rose from the ashes of the post-war world to become a rising Asian economy and a prosperous First-World nation.

This is a very different question, and while it may seem like I'm splitting hairs, to historians, the way the question is worded is very important because it determines the parameters of what we're looking at.

It is quite strange that Imperial Japan had its own share of ultra-nationalism during the second World War and committed its own atrocities like the Rape of Nanjing or Unit 731 but when we think of Japan, we often think of Tokyo and its technologically advanced notion and even its own culture such as anime, manga and even Eastern philosophies such as Buddhism and Confucianism and Zen and the Samurai during Imperial Japan that fascinated the West

Again, none of these things are related. Thus muddying the question. We can pull together a random assortment of things related in, say, German or Egyptian, or Vietnamese history and culture and come up with a rather strange assortment of concepts. Knowing about the existence of the Berlin Wall, schnitzel, and Beethoven would do little to form any kind of sensible picture of Germany.

While the Japanese military isn't my field of study, I can say as a historian that there is a series of events that historians can look at and point to that were major and minor, direct and indirect, causes of these events. The Rape of Nanking was a horrific war time event. Manga is a post-war artform. Confucianism and Buddhism are imported 5th Century BC philosophues. Samurai were a class of warriors that evolved out of the Bushi traditions of the medieval era and rose to feudal lords. These things have very little to do with each other and serve to muddy your question.

To answer the question "How did Japan go from defeat after World War II to one of the most technologically advanced nations in the world?" I'd point to Embracing Defeat by John Dower, In the Realm of the Dying Emperor by Norma Field, and Hirohito and the Making of Modern Japan by Herbert Bix. The Cambridge History of Japan is massive and unwieldy, but it will cover the vast majority of topics you skimmed through - Confucianism, Buddhism, the development of Zen, Samurai, World War II, and possibly mentioning manga in passing. It is rather large and is best used as a reference work.

tl;dr being that Japan was bombed into oblivion by the United States, and was then reconstructed as a democratic, mostly-demilitarized state that was given its own version of the MacArthur Plan, where the United States pumped money into the country to restore its infrastructure and be its front-line base as the Cold War set in.