Is it possible to check the progress of of a currently running clamAV scan

The only solution to any compromised system is a wipe and reload. It's not your system anymore - regardless of what scans are made.

I've noticed the trouble might come from apparmor. I was trying to setup clamfs for my home dir and it just kept complaining. Then I created an apparmor config file for it worked :)

$ cat /etc/apparmor.d/usr.bin.clamfs 

In simplicity I copied clamav armor and modified to clamfs - guesswork:

#include <tunables/global>

/usr/bin/clamfs {
  #include <abstractions/base>
  #include <abstractions/nameservice>

  # LP: #433764:
  capability dac_override,

  @{PROC}/filesystems r,
  owner @{PROC}/[0-9]*/status r,

  /etc/clamfs/* r,
  /etc/fuse.conf r,

  /usr/bin/clamfs mr,

  /tmp/ rw,
  /tmp/** krw,

  /var/run/clamav/clamd.ctl rw,

  # Allow home dir to be scanned
  /media/disk/* rw,
  /media/disk/** rw,

  # Site-specific additions and overrides. See local/README for details.
  #include <local/usr.bin.clamfs>
}

I also copied the /etc/init.d/skeleton to /etc/init.d/clamfs-home and edited to my intuition's best liking, made it executable and called update-rc.d clamfs-home defaults. Then executed with /etc/init.d/clamfs-home start and yay! Let's see if it comes back after reboot. What I'm wondering about is how to run clamfs with a non-root user...