Works on 4.1 AOSP/JB ROMS ONLY
1.Copy the file to the /system/app folder on your device using a root explorer like ES File Explorer or similar.
2. Then, set the permissions of the DeskClock.apk file to RW- R– R–. However, before you copy over the APK, make sure to rename the original DeskClockGoogle.apk file (and also DeskClockGoogle.odex if the file is present) to something else to back it up, which you can then restore if needed by simply deleting the new file and renaming the old one again.
3. Reboot your device to be able to use the new clock.
If you still got problems, follow this--
Flash the zip. Reboot.Delete the original clock. Rename the new clock to DeskClock.apk( like the old one) Then delete /data/data/com.google.android.deskclock. Reboot. Now the both the clock and widget will work perfectly.