There is no direct way to do this with any Adobe products. You are effectively trying to undo the separation process that created the pages you have. To do this other than via rasterization with Photoshop would require software that could analyze each of the objects on each of the separations and combine matching text, vector, and raster objects back into single objects with the color values taken from the separations.
Conceivably you could make each page into a layer and turn on overprint for absolutely all objects in each layer, although this would yield a rather awkward PDF file that might not give you the results you are looking for.
Thanks Dov. I was afraid that might be the case.
I came up with a clumsy work-around in Illustrator, using each channel as an opacity mask for a solid block of cyan, magenta, etc. and setting the resulting group to multiply. It is rather clumsy, though, and I’m doubtful that I’ll be able to create a script to automate it for a large number of files. As this is purely archiving of files from nearly a decade ago, I’m not too concerned if the resulting PDFs are somewhat awkward. The important thing is that they’re there and are readable, for the sake of posterity.
Thanks for your insight.