You have to understand HOW and WHEN and WHY a coil produces a waveform when a magnet passes over it.
I have explained this in my article FARADAY TORCH and it is much more complex than has ever been explained.
In the end you can simply connect all the coils together with a diode in the positive or bridges on each coil and they will all feed into a single output. You are never going to get 3-phase to work as the number of coils and magnets has to paired-up.
One thing you are lacking is the understanding of the term MAGNETIC CIRCUIT.
This is the at of collecting and directing the magnetic flux from the magnet so that it passes down the centre of the coil. Only this flux produces a voltage. And the strength of the flux determines the current. And the final value of current that flows is determined by the voltage and the resistance of the load.
Voltage is only produced when the magnet is coming towards the centre of the coil. Nothing is produced when the magnet is on top of the centre of the coil and a reverse voltage is produced when the magnet passes across the other side of the coil. Air will only let a certain amount of flux pass down the centre of the coil. Soft-iron core will allow 100 to 1,000 times more flux to pass down the centre. But this flux must be carried away, out the back of the coil and passed around the side of the coil to meet up with the magnet. It's a little bit like the flow of water. The magnetic flux increases and decreases as the magnets spin and this flux must be able to move around in its own circuit.
That's why the coils should be as far from the centre of rotation as possible. Because the magnets pass the coils at a higher velocity and the faster the flux can move around its own circuit, the higher the voltage and this will allow a higher current to flow.
These are all things you should have experimented with before venturing into a final design.