The API docs can be found API-docs. API requests need to be sent to api.metacpan.org.
http://explorer.metacpan.org/ is an easy way to try sending queries to the back-end.
Requests to have modules removed from the CPAN should be directed at the PAUSE admins. Keep in mind that, if a module contains sensitive information, just deleting it from your CPAN directory is not enough, as it will still reside in the BackPAN.
If the PAUSE admins approve your request, have them CC email@example.com so that we can push the right buttons to have your work removed from MetaCPAN as well.