Ok I can see where your problems are.
You need to go back to non safe mode and install the official 906 update. Then root that and carry on from there.
I have the update but not online, I think.
The links are mostly dead I see unless some one can help you out.
To install the 906 update, place the file on your internal sd making sure it is named update.zip. reboot holding x and choose the update from sdcard option and let it go, wipe cache and factory reset. Reboot, root with motofail, install safestrap and recovery, reboot into recovery ....
Wipe cache/factory rested a few time
Wipe dalivk (in advanced)
Flash rom
Reboot
Done
Lemme see if I have the update online.
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