Hi again Jeff,
The first thing I would do is to check if the same situation happens with a differente browser (Firefox, for instance).
Then I would run Disk Utility and let it verify/fix permissions and verify the drive. Then check if the in-browser PDF viewing functionality has returned to Safari.
If not, I would be to look in your home directory in the Library/Internet Plug-Ins folder, and ensure it is empty.
If it does not resolve, I would reinstall the latest version of Adobe Reader (XI) to have the most current Adobe PDF Viewer plug-ins installed. Older plug-ins may clash with the Quartz PDF plug-in that Safari uses by default; resulting in neither plug-in working in Safari. This may explain why a differente browser would work fine.
I have both plug-ins installed and the Adobe PDF plug-in over-rides the default OS X PDF viewer in Safari 6.
I find that the Acrobat plug-in offers more in-browser functionality for Safari.
Hope this helps.