Communicate link between Java and ABAP Stack for https

I have configured https in both the java and abap stacks (we have a double stack configuration).  Due to our future configuration I have changed the hostnames to fully qualified hostnames per SAP instructions. 
The question I have is does anyone know what RFC destinations or JCo settings I need to change to make https complete?
I have the problem where when I fire off the Integration Builder from within the ABAP stack (SXMB_IFR) I get a straight hostname (no domain name).  Where is this configured?  Any help is appreciated..

Check the exchange profile (Administratio tab in /rep/start/index.jsp page; you will have to enter it manually since it is throwing error from SXMB_IFR).
Regards,
Henrique.

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