I see a lot of active spots in the Indy doc, Swatches. Some colors have CMYK description, some Lab. You have some .ai links, probably with RGB definitions.You're best to start by converting the Indy Swatches to CMYK and process, prior to PDF export. If an Illy link does anything odd, open it and convert spots. Just gotta clean up those crazy swatches, mang.
Man, the designer of this piece should go to the hall of fame! I mean look at that spot color gradient in the back. Brilliant!!