I guess my main issue is that there's no mention of Amun/Amen at all from the end of the Egyptian pharaohs like Amhenhotep (who added the amen to bring back amenism in the popular culture) until then it's mentioned in the Hebrew bible. That time gap leaves questions in my head, I guess.

However looking at it more and laying it out like a timeline, I am seeing this lineage of passing the torch:

Amun / Amun-Ra worship - 1600BC to 1100BC

Tutankhamun - 1325 BC

Amenhotep - 1100 BC

High Priests of Amun - 1080 BC to 775BC

In the Bible the Books of Chronicles (16:36), it is indicated that around 1000 BC, the word is used in its religious sense, with the people responding with "amen" to hearing the blessing: "Blessed be the Lord God of Israel from now and unto all eternity".

Mention of worship of Egyptian god of Amun as being forbidden in the Bible's Book of Jeremiah which Ends in 586 BC

Amen meaning "so be it" is first mentioned in Hebrew Bible book of Numbers - Written in the 400s BC

So I guess when I lay it out like that, the gap between Amenhotep and the Hebrew Bible mentions, doesn't look as big a gap as I first thought, and that High Priests of Amun link actually covers most of the gap between Amenhotep and the Bible.

I think I'm relatively convinced of the lineage of the sound itself. Now the only real question is if that still has any meaning in relation to the original. I think it's a stretch to say people are literally praising the ancient Egyptian god Amun when they say Amen at the end of their Christian prayer. But that is pretty clearly where the word itself and the religious connotation came from. Very interesting. Thanks for making the OP. I am going to have to read more about this.