James,
I've also raised the maximum number of open file descriptors for the debian-tor user. In /etc/security/limits.conf I added debian-tor soft nofile 65000 debian-tor hard nofile 65000 I'm not sure if this worked because (even after reboot) sudo -u debian-tor bash ulimit -Hn returns 4096.
I'm currently not in front of a Debian box but I believe you will need to change the pam.d configuration, the limits module is imho not loaded in the su(do) configuration.
Renke