How can I create a Certificate Request Signed by a different algoritm than my private key?

Issue

• Need to be able to generate a cert request using an *existing* key (i.e. the root's existing private key) that is signed by something other than the default MD5 algorithm
• If the java GUI is used to create a request (pretend the cert is a subordinate CA so the GUI presents a request rather than
  automatically signing it itself), the request is MD5
• If certutil is used do the same thing, it comes out as SHA-1
• Cannot find any option in certutil to use an arbitrary signature algorithm (e.g. SHA-256).