Restore 10.8.2 to original developer settings
A common development configuration these days is to use separate guest OSes for development and testing.  With so many different OS's and configurations to test on, it seems like the only viable single-cpu solution.

In my personal experience, I tend to have the host OS tailored to looking up documentation and one Guest OS specifically for Development.  Then for each OS I will be testing on, I get the OS install image and make a new VM.  Those Guest OS's I modify as little as necessary to ensure their stability.

I still keep all my important files on the host OS's file system so that Time Machine will still pick them up.  Nonetheless, if you're hosting Mac OSes, a Time Capsule or some sort of shared AFP would still be viable if you chose to back them up.  I don't include the VM boot disks in my backups for the host OS - they change often and are rather large.

Generally I regard VMs as a disposable OS.  After initial configuration, I archive the VM boot disk and only touch it if I need to restore.

Also, if you're using VMWare, you can use Snapshots before installing your packages.  This is a good deal more convenient than doing a fully Time Machine backup, as is often want to do after messing with system files.

It sounds like you're not past the point of no return on your host OS.  You can probably still go this route, and you might find it better in the long run.