As long as the desktop is running, you can start...
Then sort by CPU usage. Or memory. Keep looking what uses most or non-ordinary high amounts by comparison.
Install some tools.
sudo apt-get install htop iotop
Go to a virtual (text) console. (https://www.whonix.org/wiki/Desktop#Virtual_Consoles)
VirtualBox host key + F1 or F2, F3 etc
(right control is default)
sudo iotop -a
Keep looking. See if any processes use and ridiculous amount >= 50% or more.
Also, keep watching syslog.
sudo tail -f /var/log/syslog
If it shows anything interesting. Or post the syslog here.