I'm not sure whether you got this resolved or not but it typically sounds like a NetApp Global Support problem. However, you mention abouted destroying the default root aggregate and then re-building it and so on... this may only install the "light-weight" ontap so you may want to re-install the ontap over the top to give you the full features again.
One other thing regarding the System Manager connections.... you may want to ensure (probably a bit too obvious) SNMP details are correct on both the controller and the GUI.
Let me know if this of any use. I'm a little rusty on the PS side of thing now
One other thing to try is running the cf-config-checker & config-advisor (previously known as wiregauge) tools to ensure both controllers are equally configured. These tools are downloadable from the NetApp Suport website (http://support.netapp.com/) under the tools section. even if that doesn't help this issue, it will potentially avoid any other miss-configuration issues.