Have you solved your problem? I am in your shoe now after I accidentally broke the fan connector and have to solder it. But I didn't mark the order of those wires, have been only able to make it run at full speed.
I am pretty sure all thermo sensors are in position and connected.
Here I write down some findings, hope someone else would also help find out right order, at least with that we can continue problem-solving.
1. Pin order in a typical 4-pin fan, Page 17 in http://www.formfactors.org/developer/spe...
2. Disassemble the fan I can read the purpose of each wire, from the PCB board:
They are GND, PWM, O/P, VN.
3. According to the spec in the specs doc above, pin 1 is for GND. But when I look at the logic board of Mac Mini:
the arrow shows the Pin 1 (pointed by "V"), GND is NOT connected to Pin 1, but Pin 4.
I don't know what do "O/P" and "VN" mean, if I assume PWM should be Pin4 as the "control" described in the specs doc, and solder GND to Pin1, neither order of the rest 2 wires doesn't work.
Now the order is:
VN -> 1 (the "V" side)
O/P -> 2
PWM -> 3
GND -> 4
and it runs at full speed. smcFanControl gets no rpm reading.
Hope this helps us go further. Probably the quickest answer is if someone else can tell us if the 4 wires maintain their order all the way to the connector.