You cannot put a manual adjuster in the system if it is split as it is out of the factory. You need to totally re-set up the system.
Two ports on the master should lead individually to the front brakes, the third should go back on the car. There is a fourth that you can block off with a bleed nipple.
Bear in mind that all lines out of the master cylinder are at the same pressure.
The third line is where the bias valve is put. The bias valve reduces the fluid pressure after the bias valve. You will only need one flexible line on to the beam. There should then be a tee on the beam that puts lines to either side, via flexis to the rear brakes.
You can use the cable-change gearbox with the standard pedal box, using a Seat Toledo 16V clutch cable, gearbox bracket and actuator arm. This is what DannyP and I run on our 'boxes.