Default [Q] Regain System Write Capabilities?

Long story made short...

I've been sitting on my stock rooted 4.1.2 (1.29.651.10). I used the Viperboy Zip to disable the system write protection.

Yesterday I finally decided to update.
I made my nandroid, relocked my bootloader, and ran the 1.29.651.10 RUU to get everything back to stock.

I booted into system, took at the sprint updates. On 4.4.2, everything seems to work besides the lockscreen weather widget. (IDK)

Re-unlocked, re-flashed TWRP, re-rooted and proceeded recovering my titanium backup files.

While I do appear to have root and can make modifications to the system, they all restore themselves upon a reboot. Is there any easy way to get system write access back? I am unable to remove the bloatware and make other modifications to the system right now?