The prefs can be deleted in C:\Documents and Settings\Your User Name\Application Data\Adobe\After Effects\9.0 for AE CS4 on Windows XP, for instance. On other operating systems the path is different, but the procedure is the same. Delete the Adobe After Effects 9.0 Prefs.txt and AE wil lrevert to factory setings. in your specific case, also delete the OriginalUserWorkspaces and ModifiedWorkspaces folders.
> I did something that has caused very poor quality conversions to .PDF, and I can not find the path described below to reset my Adobe to Factory Default.
This is an After Effects forum. I think that your question is better suited to another forum, since After Effects is not usually what people use to create PDF files.
Which application are you using to create PDF files?
Here's a link to the forum home page, from which you can select the appropriate forum for the application that you're using: