Ehm, maybe you don't need a pull up resistor:
To measure the pull up and current sourced from the fan, power the fan to 13.2V and use a DMM
To verify the pull up value in the fan, measure the voltage between pin 4 (control) and pin 1
To verify the current sourced by the fan, measure the current between pin 4 (control) and pin 1
1. The trace from PWM output to the fan header must not have a pull up or pull down. The pull
up is located in the fan hub. The presence of a pull up on the motherboard will alter the fan
response to the PWM Duty Cycle. In some cases this may prevent the fan from achieving
full speed even with the Hardware Monitor device issuing a 100% duty cycle.
If you use the fan by it self, so without the Rpi, and you connect the ground and the pwm pin to each other, does it work or is the fan running at lower speed?
The other possibility is that you need more current for the base of the transistor. But I didn't calculate that.
By the way, it could be that you need to invert your pwm signal. What I mean by that: 0% == 100% and 100% == 0% (Rpi <> fan)