If you were root when you removed ~/.cpan you should have been asked a series of questions when you tried to install cPAN again. One question should have been to choose one or more URLs for CPAN source. Get a list of mirrors and status here http://mirrors.cpan.org/.
If the ~/.cpan directory now exists, then check the URLs in file ~/.cpan/CPAN/MyConfig.pm and make sure there is one or more valid CPAN sites there.
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