How do you get IIS5 to serve PDF files when I navigate to the file I get a 404 error.
Follow the steps under Adding MIME Types to IIS 5.0 See if pdf is already defined in the list you get after press File Types, otherwise continue following the steps to add it. There is a whole list on that page of various file types to add, for pdf you will want extension pdf and type application/pdf.
In the past I've had issues with IIS not allowing certain file types to be accessed because their extension and mime type weren't defined in IIS.
Although PDF is everywhere today, I guess IIS 5 may not have had it listed by default, or it was removed on your machine at some point.
You may need to setup a MIME type for PDF files in IIS, so that it knows how to serve them. This article has instructions on doing this for each version of IIS.
Also, if you have things like URLScan installed for IIS you may need to set it to allow the pdf extension.