Drastic changes between the Sages and the written Torah

I study a lot of external books and Philo of Alexandria, etc., and I often encounter changes that in themselves would not bother me if they were publicly known, and the rabbis would say that we nevertheless trust the sages, etc. But it seems that no one has a clue, and the rabbis are in denial because it paints the sages in a really bad light.
Even about an eye under an eye that is guarded by embarrassed people, the Rambam says that it was truly the public that was incapable of hearing (and there was an ultra-Orthodox rabbi who had his lessons blasted for even talking a little about it)
And I’m talking about the fact that in all the external books our calendar is the shemish calendar and without a leap year and the leap year is indeed not mentioned in the Torah, this month for you, the head of the months, is like the mitzvah to remember the Sabbath on weekdays… the third month, the fourth month, and not like the commentators, because the reality that the spring month will not come on Passover does not make sense according to the shemish calendar… apparently only at the end of the Second Temple did they change this
And Philo has dozens of examples of prohibitions or commands that do not exist in our country.
To fish, a woman who is a prostitute and a prostitute will not be taken as the same, a prostitute who commits adultery, and this makes me think, so is the whole concept of prostitution an invention of the wise?
For a perverted woman, there is no mention of any evidence of connivance or evidence of contradiction, from the exactness of the verses, especially since she did not die miraculously, but rather interprets the pinching of the abdomen as infection and inflammation.
Only 6 relatives are explicitly listed for whom a priest defiles himself! Apparently this was before the sermon of Chazal who defiles himself for his wife. And unfortunately, there are many more examples.
I’m at a loss and feel as if Judaism was “hijacked” at the end of the Second Temple by a group of “Pharisees” and suddenly I understand why they had so many opponents and I show empathy towards the Sadducees, Karaites and other groups that I don’t know very well, because they were so well-regarded. I think to myself, they would probably call us Reformers, not Pharisees.
I really, really thank the rabbi and apologize if the words were written in confusion and emotional turmoil.