Wow... thanks for the great post and tutorial ishwest! Nice case, PCB and script work... I especially like the modifications you made in creating the monitor script
I did very much the same thing with fan control, just avoided software PWM as I don't see the benefits in this particular application. On a system with a brush fan, or a proper four wire PWM fan, yes, maybe, but I can see the brushless fans dying an early death because they are intended to be either on or off, not somewhere in between
The idea being that as the temperature rises, so does the fan speed, meaning it stays a lot quieter, only going full bore when it really is needed. I instead have mine running at (would you look at that!) 55c and cutting out at 38c. I intend to add a little more to it where it keeps running for say a minute once it hits the low end, to minimise on/off oscillation when it does heavy work.