[Q] Unlocked/tampered, and bad root / Phone works fine topic

Hi, I messed up my HTC one M7 , it's AT&T (works on T-mo sim) the phone works but shows tampered and it's badly rooted.

Long story short : I unlocked the boot loader and installed Team Recovery then rooted my HTC, everything works fine ( no tampered, and root works like a charm ) .
When the camera started showing pink/purple in low light , I wanted to return the phone to HTC to fix it, so I wanted to return the phone back to stock so the warranty will cover the repairs, I Relocked the bootloader and tried to update the phone using RUU_M7_UL_JB_50_Cingular_1.26.502.12.exe , the update didn't go through and the Updater crashs everytime I try . the phone boots fine and works fine but now shows Tampered and for the sake of me I can't get it to root it again, I tried to install SuperSu and SuperUser from Team recovery again, everything installs fine but when I use ROOT Checker it says : Sorry! Root access is not properly installed on this device .

How can I fix this and go back to stock ? I can't get S-Off because the phone is not rooted properly . Please help, Thanks you

Some useful Info :
I used Windows 8.1 both times ( to unlock and root successfully ) and (Relock and go back to stock miserably ) but I have Linux Ubunto ready on a live USB just in case it's needed to fix this problem .

Android Version 4.4.2
Sense version : 6.0
Software number : 5.12.502.2
HTC SDK API level : 6.20
Kernel version : 3.4.10-g9ec8f5a root@abm021 #1 SMP PREEMPT
MID: PN07120
CID: CWS__001
Hboot : 1.57