What would cause a zener shunt regulator to have Vout < Vz?
Just a guess, the original Zener diode was a bipolar device and the replacement that you purchased is unipolar.  That means that it looks like a forward-biased diode on one direction and a Zener diode in the other.

You can fix it (sort of) by interposing a bridge rectifier between your replacement Zener and the magneto connections.  You will want to build the bridge yourself using Schottky diodes to minimize the added voltage drop (which will show up as higher-than-desired headlamp voltage.  

Or: purchase another of those Zener diodes and connect the two Zeners in series back-to-back.