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I'm experiencing the same issue. I try to install the patch using clockwork and the installation aborts. I have rooted, bootloader unlocked, verizon xt907 with CyanogenMod 10.1.3. Any ideas?

"Mounting your /system partition...
Checking Existing Install...
Installation Aborted!
You tried installing the patch in an empty partition!
You have to install the patch after installing a rom!!!
Deleting temp files..
Unmounting /system partition... "