Here's a suggestion, if you're running Windows XP, run a system restore to the point BEFORE you noticed the changes. Then, once that is done, acquire your bookmarks, everything you need, if it's still there that is, and put them on some sort of removable storage. A flash drive, floppy drive, burn it, whatever you gotta do. Then reverse your System Restore and you'll be back to your current configuration. The reason why I say to move the files out of the system is that SysRestore has a sneaky tendency to remove certain new files copied on the system. Reversing the system restore will get you back to the present though, and everything will be intact. Then just inject your files in the correct places and you should have your stuff back.
Of course, you'll need to have System Restore turned on and on the drive you installed Firefox to. If you're not running System Restore, then you'll be better off looking for a program called "Restoration". It will scan NTFS recently deleted files, and possibly help recover them. It's a bit old, but it's the best FREE file-recovery tool I've ever used.
Something else to consider. If your bookmarks.htm file was overwritten, not deleted and re-created, there's probably no hope of getting it back unless you have System Restore on and at the ready.