The wires and functions of a 4-pin fan are:
Pin #1 (Black) Ground
Pin #2 (Yellow) +12 VDC fixed
Pin #3 (Green) Speed Pulse Signal
Pin #4 (Blue) PWM Signal
The signal in Pin #3 is a series of pulses (2 per revolution) generated in the motor and sent back to the mobo on this line for counting so that it can display the motor speed. This signal is NOT used to control the speed. Often mobos will monitor this line in case it shows no pulses, in which case it will issue a warning of fan failure.
The signal on Pin #4 is the PWM signal from mobo to motor. I believe it is a 5V signal like a square wave (it is either on or off) BUT not "square" in the sense that its % On time is not always 50%. Its % On time is what is varied to control flow of current from the 12VDC supply through the motor (via a small controller chip inside the motor housing). The more time the current actually flows, the faster the motor runs. I do NOT know details, so you'd have to find that if you want to create your own PWM signal.
There may be an easier way for you to do this without re-engineering the controls yourself. You CAN use the mobo's SYS_FAN port(s), but not in automatic mode since you prefer to DIY. And since you want all the cooling fans to operate under one control, you will need two things:
(a) A utility that runs under Windows and gives you access to fan control settings - this usually is included on the CD of utilities that came with your mobo. It will allow you to pick any of your mobo SYS_FAN ports and set its output (fan speed) to a fixed value of your choosing, also giving you a display of the fan's actual speed based on that pulse signal.
(a) A 4-pin special type of splitter also known as an adapter like this:
http://www.newegg.com/Product/Product.aspx?Item=N82E16812423165&cm_re=4-pin_fan_splitter-_-12-423-165-_-Product
Most mobo fan ports can power up to 2 fans, but you have 4. This adapter does two three things for you. First, it gets power for all (4) of its fans from a 4-pin Molex output of the PSU (can power MANY fans), and takes no power from the mobo SYS_FAN port. Secondly, it picks up the PWM signal from one mobo SYS_FAN port and shares that to all 4 of its fans - this does not overload the PWM signal. Third, it ensures that of its 4 fans, only ONE gets to sent its speed pulse signal back to the mobo (to avoid problems with the counting circuits) - the speeds of the other three simply cannot be monitored. That also means that possible failure of any of those three unmonitored fans cannot be detected for you - you have to check from time to time.
If you do it this way, you will have your manual control of all 4 fans as you wish, without having to design a controller system (you use the one already built into your mobo) and without having to install a third-party fan controller unit in a non-existent case.