Ubuntu-base and Ubuntu-desktop are, as far as I can tell, not packages in themselves but enormous lists of dependencies so you can just install Ubuntu-desktop to get Gnome, GTK, Metacity, and all the paraphenalia associated with them. You need to get rid of both of them, if you've uninstalled some of the software they 'depend' on.
Others, I'd mark for reinstallation. That'll bring back the things they need, which fixes the breakage.
You may also like to look for Ubuntu versions of the Deb files you installed before. That'll make everything run smoother.
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