FBB and Craig are both awesome and we are lucky to have them participating here.
About the Save As, I always saved multiple versions of my project along the way, but then a certain company told me that my string libraries (Vienna and Hollywood) were performing poorly because I needed more free disk space. So, I took a Saturday to move all but the most recent versions of every song to an external drive, keeping only the latest version of each on my internal drive (and backed up externally, of course). I then defragged the disk.
This all made absolutely no improvement in the string performance.

I seemed to be cursed.
I think the only solution is to buy a new PC (with SSDs for sample libraries), and install X3 fresh. (I will also try to install both my V-Studio I/O and MOTU Interface so I can toggle between the two. There is a theory going around that the V-Studio I/O causes a lot of my problems, but I do not believe it. The issues seem to be Sonar related and I know of no other Roland interface users with similar problems.)
Needless to say, this would be costly and the time would be significant, since my Vienna libraries alone will take two days to install, and I have many other libraries. I will also have to go through all the onerous authentications (like NI!) and make sure eLicenser and iLok are working.