I just tested the latest 2.4.0 build and it does not seem to work with a CSR that has been generated on a separate system also there is no option to choose server or user signing. To solve my issue I:
1. Created the server certificate on PFSense (make sure it is set to server cert, the default is user cert)
2. Exported the new cert
3. Exported the new Key
4. Moved them to my JBOSS server
5. Converted they two to a PKCS12 (openssl)
6. Converted the P12 file to my keystore (Keytool)
Example:
mv /home/ncadmin/par.local.enms.net\ (1).crt ./par.crt
mv /home/ncadmin/par.local.enms.net\ (1).key ./par.key
openssl pkcs12 -export -in par.crt -inkey par.key -out par.p12 -name par_na_crt -CAfile RootCA-Pfsense.crt -caname root
keytool -importkeystore -deststorepass chgme -destkeypass chgme -destkeystore truecontrol.keystore -srckeystore par.p12 -srcstoretype PKCS12 -srcstorepass chgme -alias my_alias