After upgrading from 3.6.16 (Mac) to v. 4, the "organize Bookmarks" menu item is gone. Also, the Downloads window will not come up (I have reset the Toolbars as suggested elsewhere.)
The above says it all:
No "Organize Bookmarks" item at all in the Bookmarks menu.
I have the prefs set to display the Downloads window when downloading, but it doesn't appear. Downloads do happen correctly. Clicking on the Downloads item in the Tools menu does nothing. I reset toolbars as suggested somewhere else on the troubleshooting site - no joy.
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"Organize Bookmarks" has been renamed to "Show All Bookmarks" in the bookmarks menu.
For the other issue, you have tried some of the options listed, bit for other things to check see https://support.mozilla.com/kb/Downloads+window+does+not+open
Thanks re: Bookmarks.
After going through all the routines suggested in the link above (and other related links,) I got the Downloads window to open when making a new download, but clicking on Downloads in the Tools menu still will not reveal the window manually.
Try to move (delete) the Firefox plist file.
Go to "Library > Preferences" and remove the plist file for Firefox (org.mozilla.firefox.plist).
No joy.