Two ideas come to mind, but I don''t KNOW that either of them will work.
1) Perhaps one of you can sell their half to the other (at least on paper) so the 100% owner can then document it in their country.
2) Could a "Flag of convenience" suit your needs? I think Panama and/or Nigeria allow foreign vessels to register as theirs, and are thus able to get documentaion and insurance.
~ Good luck, and happy sails to you ~ _/) ~