Sorry for the lack of follow through but I got it working and production took over.
To resolve the issue of saving an Illustrator eps as pdf and the pdf holding onto the page size as opposed to the bounding box, within Acrobat in the Crop Pages dialog, selecting "remove white margins" crops the document to the bounding box of the object.
Once the bounding was corrected the files showed up in all previews and final files. The only thing to watch for is when uploading files to MarcomCentral you will need to deselect the placed pdfs because MC will error indicating only one pdf can be uploaded and that being the template itself.