Is there a way to create spot colors (and separations) from a PDF file that is CMYK? This is for the 2016 version of Acrobat Pro DC

With a Preflight Fixup

Use the Output Preview panel to determine if the objects/type are RGB or CMYK. (Change the show value to RGB/CMYK)

Open the Preflight Panel

Highlight the Wrench icon for Single Fixups

Select (from the) Options > Create New Preflight Fixup

Type Spot in the Type of fixup find field

Fill in the values for the cmyk - Name the fixup - Spot color name can be Pantone format or generic - click OK to save the fixup

From the Preflight Panel (from the Select Single Fixups wrench icon tab) > Color Spaces, spot colors, inks - run the Fixup

Verify the result(s) with Output Preview