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In your profile folder, you can find "bookmarks.html". Your profile folder for mozilla is in /home/username/.mozilla/profilename (most likely "default", unless you created an additional one)/random string of letters and numbers/. Your profile for firebird/firefox is /home/username/.phoenix/profilename (most likely "default", unless you created an additional one)/random string of letters and numbers/.
The dot in front of .mozilla or .phoenix means that these are hidden folders, so turn on "View/Show hidden folders" in your file manager if you don't see them. You can just copy the "good" bookmarks.html file to the profile folder of the browser you want to see it in (i.e., from your Mozilla profile folder to your Firefox profile folder) and they will show up.
You might also want to actually choose "Manage Bookmarks" in your updated Mozilla-- Mozilla should have used your original profile, unless you created a new one, so if you don't see your bookmarks it might be because the newer version handles bookmarks slightly differently (the name of the Personal Toolbar Folder is different; now it's the Bookmarks Toolbar Folder), so if you actually open the Bookmark Manager, you can see if the bookmarks are there, but just not visible in the toolbar or whatever, and set the correct folder to display them.
If you set up a new profile (or Mozilla did; it's possible that the default profile has also changed name from "Default User" to "default" or vice-versa), you can start mozilla with "mozilla --profilemanager" to get the profile manager and see if your original profile is still available.
Lastly, if you were using the old Mozilla as a different user than the one using the current Mozilla, the bookmarks are in the profile directory in the other user's $HOME$, not the new user's.
Anyway, they should be around somewhere. Mozilla is very good about not erasing or overwriting such things just because you updated. That's the very reason they are kept in your $HOME$ rather than the application folder. If you still can't find them, try a "locate bookmarks" and see what you come up with.
Hope this helps.
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