Too much info error... So it's possible to flash an OTA over my rooted stock rom using TWRP?
Since the OTA is already downloaded to /data/data/com.htc.updater/files can I just copy it to the root folder and then flash it with TWRP?
No, TWRP cannot handle an OTA completely. You have to reflash stock recovery.
And even if you reflash stock recovery the OTA could fail to apply.
Have you modified your system partition after rooting? Any mods that install to system instead of data?
If you have modified the system partition the OTA won't apply. You have to reset to stock, i.e. by using an RUU