I'm not sure what you think you are reading there, but verse 1 says the Logos was in the beginning. It's not until verse 14 that John then takes this eternal Logos which is identified as Divine in the 3rd clause of verse 1, and then clearly states, "The Logos became flesh", which is a direct reference to Jesus. So, "The Logos is God".... "The Logos became flesh." You don't see it's a continuous thought from verse 1 to verse 14, identifying Jesus directly with the eternal Logos?
Correct. The flesh is temporal, Spirit is eternal. Spirit became flesh does not mean Spirit ceased to exist. It means it took a temporary form.
You seem unfamiliar with the doctrine of the hypostatic union, which is that Jesus Christ was both fully man and fully God. Fully man means he had a beginning, born of his mother in history. Fully God means he was eternal Spirit. Etc.
Regarding the OP, I pointed out how you can just as easily make a mockery using dualistic language to describe nonduality when you imagine the Omnipresent God, meaning God is everywhere at all time at once, doesn't exist somewhere, such as in you, or AS you. Is God a block of swiss cheese and you exist in the holes where God does not exist? How can God be omnipresent, yet be imagined as "outside" of you?
Please explain that, and then take a look at how you butchered the meaning in your OP by trying to force fit nondualistic truths into a construct of dualistic language, yet at the same time, you leave the Omnipresent God that somehow is imagined to not exist everywhere alone? Can you make God everywhere, but not everywhere at the same time? No? Then how is your OP any better at speaking truth? I think the atheist that denies God exists would have an easier job at that than you do.
Sauce for the goose, is sauce for the gander, as they say.