If the Trojan war supposedly took place in late Mycenaean Greece how come Zeus is addressed as the chief god in the Iliad when Poseidon was the chief greek god in Mycenaean Greece? Furthermore how come the pantheon of gods in the Iliad has more in common with classical antiquity than it does with Mycenaean religion. To my understanding the Iliad and the Odyssey were both memorized for hundreds of years rather than written in fact Homer was a blind bard who was just telling stories he memorized and they were eventually written down. If this is true and the stories were told over centuries is the lack of Mycenaean religion due to the possibility of the stories being altered over time to be more in line with Greeces views at the time or is there another answer I just haven't been able to find.
A key premise in your question is untrue: the idea that the Trojan War supposedly took place in Mycenaean Greece.
Yes, Hellenistic (4th-3rd century BCE) Greek chronographers liked to date the fall of Troy to the 1300s-1200s BCE. And that happens to line up reasonably well with the end of the historical Bronze Age as we understand it.
But those Greek chronographers knew nothing of the Bronze Age. They hadn't the slightest idea that the Bronze Age palace culture existed, or the Hittite empire, or anything like that. Even Homer contains scarcely any trace of the Bronze Age, whether in terms of ethnic groups, individuals, or events. All knowledge of the 'Mycenaeans' was lost until the 19th century, when archaeological evidence was studied methodically and Bronze Age languages began to be deciphered.
The coincidence between the date picked by Hellenistic chronographers, and the end of the Bronze Age, is precisely that: a coincidence.
Troy had been resettled by Greeks in the 8th century BCE, and the contemporary city coloured all of the legendary material that arose around it. Homeric epic in particular is almost purely 8th-7th century BCE: in terms of its depiction of material culture, marriage customs, military equipment, inheritance customs, legal and political framework, and so on.
This naturally goes for religion too. The Iliad depicts the main civic cult of Troy as that of Athena Ilias, 'Ilian Athena', the cult established by the 8th century Greek colonists. The Bronze Age cult of Appaliunas still existed, as a cult of Apollo, a few km from the city, but Athena is right there in the middle of the city in Iliad book 6. Similar things apply to the rest of the pantheon.
(By the way, I'm not a Bronze Age specialist, but I'm not aware that the position of Poseidon in the Bronze Age pantheon is as clear-cut as you make out. He certainly held an extremely important position, but I don't know that that justifies calling him 'chief god'. Maybe you know something about that that I don't, though.)
There are only occasional snippets of earlier material in Homer. One piece of equipment (a boar's tusk helmet in Iliad 10 that matches Mycenaean-era examples); one word (anax meaning 'king, overlord' as opposed to a religious title); one village in Boeotia, Eutresis, that had been abandoned ca. 1200 BCE and hadn't been resettled. Those three things are the only demonstrable cases of Mycenaean content in Homer -- and one of them, the helmet, wasn't originally part of the epic (Iliad book 10 was spliced into the rest of the poem).
The story of Homer being 'memorized for hundreds of years rather than written' refers to the period between the poems' composition and their transcription, not the period between the Trojan War and Homer. 20th century scholars had to posit centuries of oral transmission, because in the mid-1900s the composition of the Iliad was conventionally dated extremely early. Finley thought 'Homeric culture' was 10th century, for example; but the classical alphabet only emerged in the 700s. The 'centuries of oral transmission' were invented to explain that discrepancy. In more recent decades the epics have been gradually but consistently down-dated, for a variety of reasons, especially the references to 7th century material and military culture that I mentioned above. Nowadays the normal dating is ca. 670-650 BCE for the composition of the Iliad, and a slightly wider range for the Odyssey. As a result it's possible to imagine they were written down straightaway, and some scholars believe precisely that -- though as it happens I tend to believe they were transmitted orally after that point, for at least a century, and only transcribed in the late 500s. Either way, no one's talking about Bronze Age stories being memorised. (Except for a very few, very elderly scholars, who just refuse to accept the down-dating of Homer and Homeric culture.)
(Edit: a couple of minor corrections and rephrasings)