Not sure what you trouble is exactly but try.
Open the project browser Command:AecProjectBrowser
Browse and then double click on the project to set your current project.
Save whatever drawing that was (has been) created outside of the project navigator into a temp location ie My Documents. Delete any copies of this drawing from any folder inside of the project structure since it needs to be added correctly to register in the Navigator.
Open the project Navigator Command:AecProjectNavigator
With your drawing open from it's temp location. Right click on a construct category folder and choose save current drawing as construct. Rename it.
If you still cannot open the Project Navigator pallet then I am unlikely to be able to help since I have never experienced this problem. The only thing that bugs me is the 'cannot run in a zero document state' message.