[General Questions and Answers] discoweasel:
I looked over the log and I do see a few errors which may or may not be a major problem.

Line 234

pull: /system/bin/uncrypt -> ./bin/uncrypt

failed to copy '/system/bin/uncrypt' to './bin/uncrypt': Permission denied

Line 404

pull: /system/bin/install-recovery.sh -> ./bin/install-recovery.sh

failed to copy '/system/bin/install-recovery.sh' to './bin/install-recovery.sh': Permission denied

Line: 631

pull: /system/etc/firmware/wlan/prima/WCNSS_qcom_cfg.ini -> ./etc/firmware/wlan/prima/WCNSS_qcom_cfg.ini

failed to copy '/system/etc/firmware/wlan/prima/WCNSS_qcom_cfg.ini' to './etc/firmware/wlan/prima/WCNSS_qcom_cfg.ini': Permission denied

Lines 2082-2099:

pull: /system/vendor/itson/update-binary -> ./vendor/itson/update-binary

failed to copy '/system/vendor/itson/update-binary' to './vendor/itson/update-binary': Permission denied

pull: /system/vendor/itson/resources.zip -> ./vendor/itson/resources.zip

failed to copy '/system/vendor/itson/resources.zip' to './vendor/itson/resources.zip': Permission denied

pull: /system/vendor/itson/resources.version -> ./vendor/itson/resources.version

failed to copy '/system/vendor/itson/resources.version' to './vendor/itson/resources.version': Permission denied

pull: /system/vendor/itson/keys -> ./vendor/itson/keys

failed to copy '/system/vendor/itson/keys' to './vendor/itson/keys': Permission denied

pull: /system/vendor/itson/kernel.api -> ./vendor/itson/kernel.api

failed to copy '/system/vendor/itson/kernel.api' to './vendor/itson/kernel.api': Permission denied

pull: /system/vendor/itson/itson_installer -> ./vendor/itson/itson_installer

failed to copy '/system/vendor/itson/itson_installer' to './vendor/itson/itson_installer': Permission denied

pull: /system/vendor/itson/itson-bootstrapper.sh -> ./vendor/itson/itson-bootstrapper.sh

failed to copy '/system/vendor/itson/itson-bootstrapper.sh' to './vendor/itson/itson-bootstrapper.sh': Permission denied

pull: /system/vendor/itson/integration.version -> ./vendor/itson/integration.version

failed to copy '/system/vendor/itson/integration.version' to './vendor/itson/integration.version': Permission denied

pull: /system/vendor/itson/devinfo.json -> ./vendor/itson/devinfo.json

failed to copy '/system/vendor/itson/devinfo.json' to './vendor/itson/devinfo.json': Permission denied

Basically a search for 'fail' returns this:

failed to copy '/system/bin/uncrypt' to './bin/uncrypt': Permission denied

failed to copy '/system/bin/install-recovery.sh' to './bin/install-recovery.sh': Permission denied

failed to copy '/system/etc/firmware/wlan/prima/WCNSS_qcom_cfg.ini' to './etc/firmware/wlan/prima/WCNSS_qcom_cfg.ini': Permission denied

pull: /system/etc/mmi/fail.png -> ./etc/mmi/fail.png

pull: /system/etc/mmi/fail.png -> ./etc/mmi/fail.png

failed to copy '/system/vendor/itson/update-binary' to './vendor/itson/update-binary': Permission denied

failed to copy '/system/vendor/itson/resources.zip' to './vendor/itson/resources.zip': Permission denied

failed to copy '/system/vendor/itson/resources.version' to './vendor/itson/resources.version': Permission denied

failed to copy '/system/vendor/itson/keys' to './vendor/itson/keys': Permission denied

failed to copy '/system/vendor/itson/kernel.api' to './vendor/itson/kernel.api': Permission denied

failed to copy '/system/vendor/itson/itson_installer' to './vendor/itson/itson_installer': Permission denied

failed to copy '/system/vendor/itson/itson-bootstrapper.sh' to './vendor/itson/itson-bootstrapper.sh': Permission denied

failed to copy '/system/vendor/itson/integration.version' to './vendor/itson/integration.version': Permission denied

failed to copy '/system/vendor/itson/devinfo.json' to './vendor/itson/devinfo.json': Permission denied

failed to copy '/vendor' to './vendor': Is a directory