Running out of ideas but your dmesg log (at the end) showed a USB disconnect. Double check you cables and change if possible.
1) A fresh install without any addons/customisation (bar TVH)
2) Install the LE addon "system tools" and monitor the system with either nmon, htop to see I/O and memory usage.
3) Check free memory withfree -h
4) Check you USB ports, but adding a USB device and check dmesg for any disconnets
5) Check your power supply and change if possible. Also check output of vcgencmd get_throttled if NOT 0x0 then you have issues.