I had trashed STP after moving in ~/Library/Safari/Bookmarks.plist didn't help, so I reinstalled it, and again didn't have my bookmarks or cookies. (STP didn't pick up my prefs either, but I'm not sure if it's supposed to.)

So before doing anything else, I took a look and found that ~/Library/STP/Bookmarks.plist didn't exist but ~/Library/STP/TopSites.plist did, so I moved it to the side, moved in ~/Library/Safari/Bookmarks.plist, and VOILA! (The ~/Library/STP/Bookmarks.plist I originally reported having was apparently created by me when I bookmarked FTM.)

At any rate, I've now got a usable version of STP, albeit sans cookies, which I'll recreate as I go along, and hopefully they won't disappear.

The new Great Equalizer is the SEND button.

In Memory of Harv: Those who can make you believe absurdities can make you commit atrocities. ~Voltaire