Parse the list of separations and create new PDF for each separation. How can I do this with SDK?

A hard job. There is no list of separations in one place. You would need to go through the PDF examining every object on every page. You can then make the separations. But there is also the question of what to do for each of the colour spaces (e.g. Lab, RGB...) and the problem that just deleting objects in the separation will not give correct results. I cannot really give more help on this but I will say: consider the case of a Spot Red circle overlapping a Spot Blue circle. If you just delete the Spot Blue objects, your Spot Red circle is complete, rather than being the circle only where not covered in Spot Blue. And overprint settings become very important. All this must be built on an absolutely rock solid knowledge of 32000-1, especially the graphics chapter, but also text and transparency.