Doesn't the master cylinder return pressure push the brake pedal back into position? I may be looking at this wrong but shouldn't the brake lever return spring need a stop block or be moved to where it will hold the pedal in the correct position?
I would find the proper pedal height and mount the return spring in that position so the rod stays in contact with the master cylinder. The spring should maintain tension on the pedal assembly through it's range of motion and return it to the starting position. Remember you are not going to be able to use the factory position for the return spring now that you have changed to a dual master cylinder. It will probably come down to trial and error to find the correct location for the spring.
