I did something like this to bring up PDF as-built plans of sanitary sewers when a sewer section was clicked on. I got it to work by modifying my popup .xsl file in ArcMap and then creating my layer package to bring into Explorer. I added a field in my feature class with an absolute file path to the PDF for each feature, e.g. C:\...\file.pdf (You could use an http:\\ or UNC path also).
Now when you click on a feature the popup comes up and the field with the file path to the PDF is a highlighted link to the PDF. Click on it and the PDF comes up in a new Adobe PDF Reader window.
Attached is the zipped .xsl file that I modified also. Hopefully this is of some use to you. I would be glad to hear if it works for you.