I am writting back to you because I manage to get something for my dual card computer which might be useful to you. I followed the instructions in this link http://blog.cryptohaze.com/2011/02/nvidia-fan-speed-control-for-headless.html .
It requires an extra monitor. I connected the second monitor to my TITAN and I opened nvidia-settings with sudo. In there I went to the menu XserverDDisplay configuration and I changes from TwinView to separate X. Save the xorg.conf and add the coolbit line in xorg. Now after restart you can have the option to control the fan of TITAN. After restart you can remove the second monitor. At this moment I am not sure if you need the second monitor at each restart, but for me it is ok, because I have 2 anyway. I am now running an iterative cufft based algorithm for a matrix of 8192x8192 and the temperatures are around 50C , while before they were at about 80C