a few issues here. First off, the clutch pedal SHOULD be higher than the brake pedal. Upward travel should be stopped by a rubber bumper on the pedal brackets so first off make sure the bumper is in place. On the other side of the firewall, there should be a spring pulling the Z bar back towards the firewall and a second spring pulling the clutch fork against the Zbar keeping the rod in between under tension from falling out as you describe.
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