Automation commands for Lighttpd (start|stop|restart) are charged by S80lighttpd script (found in /opt/etc/init.d/). Thus, to start Lighty with TomatoUSB, add this line to your Automount (Run After Mounting) script:
/opt/etc/init.d/S80lighttpd start
To stop Lighty before reboot, add this line to your Automount (Run Before Unmounting) script:
/opt/etc/init.d/S80lighttpd stop
Add "sleep <sec>" command to these lines, if your server starts/stops slowly.