Can't believe I'm asking this, but I can't figure out where to re-name the original project without doing a "save as" and creating a second project file.

that is pretty easy to do …
if you save your projects in their own folder just find the Cakewalk project and re name it .
it really is that simple 
 
Kenny

Thanks! That worked perfectly.
I was looking for a dropdown menu option for this inside of X3. I didn't want the project file to point to unrecognized audio files of a different name (if that makes sense) so I was hesitant to re-name it. But I guess it changes them as well.

glad that worked out for you .
sure SONAR will find all the associated audio files …
in your X 3 preferences it is a good idea to use a per project folder ,it keeps everything in one place. 
then you will have your project folder , the X 3 project and your projects audio folder  ..
this way when you change the name of your project , you can also change the name of the parent folder …
doing per project folders makes it easy to keep track … 
 
FWIW , I always end up changing the names of my song projects often  …
this is due to the reason that I mostly do instrumental music …
I currently work alone and when I start my songs , I usually give them a temporary name that characterizes the songs vibe  …
usually a good song name will come to me as my mix progresses …
 
Kenny

Use Save As in Sonar to rename a project. That way you will have a backup of the project.