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I think the problem has more to do with how Publisher handles the vector info than with anything Acrobat or PitStop is doing. I had a similar job recently where a client sent an xmas card in Publisher, and wanted a block of 'WordArt' to be printed as a metallic silver spot ink.
When I PDFed it and then opened it in Illustrator, all the WordArt shading became hundreds of little objects with clipping masks, just like you said. In my file though, the masked objects actually seemed to be bitmap images underneath the clipping path, according to the links palette. If your file is doing the same thing, that might be why Acrobat and Pitstop don't see them as tints. I think I ended up exporting the WordArt as a 1200 dpi bitmap, and then making it a spot colour monotone in Photoshop. Ugly, but hey, that's what you get when you send Publisher files.
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