Yeah I got why it was PWM, I just wasn't sure how it would change the relationship to the potentiometer resistance. I determined experimentally that when the fan is at 3V/25% duty cycle when the Pot's wiper is 17.5/76.7kOhms. Since it's at 12V/100% at 94.2/0 kOhms, I guessed that increasing the resistance of the pair or wires that gave me the 17.5/94.2 kOhms by that 17.5, would make it a minimum of 3V/25%. I don't have a 17.4kOhm resistor, I used a pair of 33kOhm resistors in parallel, for 16.5kOhm baseline resistance. I don't really understand the mechanism, but it basically works. With the potentiometer turned to minimum speed, I now read 2.5V across the fan. If I put another 1kOhm resistor in series, it should make the minimum duty cycle closer to 25%.
It's not really the most elegant solution, but it works, I just have to figure out why. I don't really understand how the potentiometer is wired up with the two diodes, and how that effects the output. Nor do I really get the relationship between that value and the duty cycle the 555 generates. Working those things out is probably half the fun of electronics though right? That's what I'm telling myself anyway.
Since I'm still at the breadboard stage, any other suggestions are more than welcome. In the mean time I'm going to try to work out how to add some indicator lights without exploding them. Thanks for the prompt feedback guys!