PeterH:
From your references to 'monetary loss', are you thinking that you're actually going to make any money out of coin mining? I think you'll find that boat has sailed long ago.You should be able to PWM control ordinary brushed PC fans, and you can use one or more DS18B20 temperature sensors and potentiometer inputs to control the fan speeds using whatever algorithm you want, and you can drive a relay to operate a relay which shorts across the 'power' button if you want. I'm surprised that any of this is necessary, though. It's been years since I bought a PC without automatic CPU temperature sensing and fan control, and I think you're reinventing the wheel. But what you're describing is not very complicated, if you decide that's what you want to do.
It wont be profitable to him since he's fronting the bulk of the cash, but he's already gotten ~100 bucks from running if for a weekend with half the intended cards. At least thats what he claims. I havent looked into it much but I know its litecoin he's mining and that litecoin is asic resistant. So it may be viable if he got the cards cheap enough. But since I'm just building the system and housing it once its finished, I dont really mind pulling a percentage for basically nothing.
The concern with using the computer to control the fans is when this project does get ported to the mining rig, there wont be enough fan headers on the motherboard and he wants to be able to remotely check the temperature and control the fans. I'm building this for the fun of it, the experience, and the fact that I get a percentage of anything the rig mines when that time comes. The remote control is something I'm going to be implementing later.
As for the fans, I just wanted to be absolutely sure that they could be controlled via PWM pin.