The multiple clipboards for copy and paste are driving me crazy. Is there some way to make ctrl-c, mouse highlight and menu dropdown->copy all do the same thing so I don't get something different depending on how I paste?
Parcellite Clipboard Manager will do what you want. Open the preferences, and check "Use Copy" "Use Primary" and "Synchronize Clipboards".
But be aware that synchronizing the selection buffer to the clipboard will necessarily prevent you from pasting text over a selection, because selecting text to paste over will replace the clipboard with the selected text.