I want to share with you how i returned to 100% stock after been S-OFF with unlocked bootloader and custom rom. I tried everything i found for doing this, but i always get TAMPERED at the end after switching to S-ON. If you stay S-OFF there is no TAMPERED flag.
What finally helped was that i found a RUU 4.09.401.3. With the custom rooted rom and revone you can easy lock the bootloader and S-ON. After that you just need to flash the RUU and everything is stock, without any trace from been other way.
This is where i found the RUU, i think it will be very usefull for many people here:
And the direct link to the RUU:
M4_UL_K44_SENSE60_MR_HTC_Europe_4.09.401.3_Radio_1 .28.40e.00.24_10.z19.40.1304L_release_383370_signe d
Big thanks to Beast78 and 666SATAN666 that made this RUU available for us.