Yes I strongly recommend you switch to 4.1, if nothing else to get access to a good number of new face morphs that aren't included in vanilla V4, but also to fix that bugged morph data.

Uninstalling your content will probably no longer work since you've renamed directories.  Most of the content distributed in zip files isn't really "uninstallable" anyhow, but you can delete the files you copied in if you knew where you renamed them to.  I don't even want to try to advise you as to which is safe to rename and which is not, because there's really a lot of variables.

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