There should be a potentiometer on your extruder controler. Unless you are using G-codes to set pwm, you need to adjust the potentiometer so that the motor and chips stay cool without loosing too much torque. They should run at a little more than room temperature. Running a stepper motor off the extruder controler does tend to be more noisy than using an actual stepper driver. I prefer to use a fourth stepper driver to run the extruder. At some points, it runs so quiet that you might not know the machine was running if you didn't see it moving.
As for the Z-axis, it sounds like you are trying to say that the axis moves backwards? You might find an option in your firmware configuration to reverse this. You can also switch the two pairs of wires so that the coils are swapped. Read the second to last section
here for more on wiring the motors.
Edited 2 time(s). Last edit at 12/05/2010 01:35PM by dazed.dnc.