My Extensions were messed up too.
Here is how I fixed it:
1. Go to users/*yourname*/Library/Safari/Extensions (easiest way is to go to Finder, click Go in the menubar, hold the Option key to reveal "Library"). Your old extensions will still be there.
2. Dub-Click on each file you want to reinstall.
3. This will take you to Safari where it asks if you want to View Extension page, click yes.
4. Click Install now on the Extension page (delete or move original file before installation to avoid duplicates)
Unfortunately, it looks like the extensions are "lost" again every time you quit Safari. Oh well, Im sure there will be a fix soon enough.
EDIT: It's worth noting that when you click the usual links to the Safari Extension web page it now opens the App Store app, presumably because Apple is going to move all extension downloads there in the future.