[papajam]

If I understand correctly, the clutch master cylinder pushrod is a half inch longer than it should be? If that's the case, that could be the problem. When the pushrod is too long, and this goes for brake M/Cs as well, the M/C piston can't return far enough to uncover the compensating port which allows fluid from the reservoir to enter the cylinder ahead of the piston. There simply may not be enough fluid in the pressure side of the system. You might want to try pulling the clevis pin from the pivot arm to pushrod. Then, while ensuring that the clutch pedal is about the same height as the brake pedal, shorten the pushrod so that the clevis pin can be installed with no pressure on the pushrod.
AFAIK, the pedalbox can be assembled only one way.