Create an interactive map, manually, using Flash, and embed it into the PDF.
To do so, first extract each layer as an image, ensuring that you use an image format that allows for transparent colors (PNG in this case). Then, combine these layers into Flash in the correct order, create your own zoom/pan functionality, and manually add points to the map to indicate that an image exists at that location. Finally, create an image viewing mechanism so that when a user clicks on an icon on the map, the appropriate image appears.
To insert the map into a PDF, first Publish your Flash application. Open Adobe Acrobat and click the Add Movie button (looks like a film strip) while on a blank page, then locate the SWF file that you created and select it. Save the PDF and your users will now be able to see the map inside the document.
This is the solution I came up with, but I won't accept this as an answer since it still doesn't feel right; plus, it's tedious to do all of the processing and programming manually rather than having a real GIS solution for this problem.