You said, "One area where I disagree is regarding the origin of Samkhya. It seems that there is an assumption that it evolved from ignorance."
I am not sure why you made that "assumption". Nowhere do I say or imply that Samkhya arose out of ignorance. In one place I specially write
"In the fertile period, around 500~600 B.C.E., ideas were being developed and exchanged between many fields of inquiry. Samkhya philosophy informed pre-classical yoga, which borrowed from Jainism, which also influenced both Samkhya and Buddhism. Each philosophy borrowed, tested, adopted, and discarded ideas and practices from each other. Eventually a consistent psycho-cosmological model precipitated out for each philosophical approach." I believe that Samkhya developed, not out of ignorance, but out an attempt to make sense of the world but, like all philosophies, it borrowed from previous thoughts and ideas.
You mentioned the yugas which I discuss in my book From the Gita to the Grail
. There are two ways you can consider concepts offered in ancient religious texts: 1) as historical truth, or 2) as metaphorical truth. If you choose the former, that is your prerogative. I prefer the latter and love the wisdom of the American mythologist of the 20th century Joseph Campbell who taught that if you read ancient teachings as literally true, then one error or inconsistency will bring the whole edifice crumbling down. But, if you read the teachings as metaphorically true, then you can mine the deeper essence of the teaching.
I prefer to follow the scientific consensus and do not believe the yugas to be historical fact, but rather, like a great poem, there is an inner truth that we can find in these stories. Thus, I cannot agree with your proposition that Samkhya survived from a prior cycle of the yugas. There is no historical or scientific evidence for that. It makes far more sense to assume Samkhya, like many of the other philosophies that arose in the Axial Age, was a collection of ideas that coalesced from the musings of spiritual philosophers in South Asia. Having said that, there is much we can learn about ourselves by contemplating this system of thought.