I don't know what I did wrong along the way but I had problems getting fancontrol to start at boot time correctly.

1. I had to go into my BIOS and disable the CPU Fan Control system. pwmconfig would detect and operate the fans and set up a fancontrol profile, but the profile was doing nothing because the BIOS was overriding the input.

2. I had to do the same renaming of the fancontrol.pid as described very early in the thread.

3. I had to use sudo update-rc.d -f fancontrol remove
 followed by sudo update-rc.d fancontrol defaults to get it to start correctly at boot time.