For a zener regulator to safely clip a pulse, it should be set up something like this:
The resistor should probably be 1K or so. This is well high enough to not affect the coil drive signal, and well low enough not to make much difference compared to the input impedance of Microsquirt. The output from this ciruit should be a squarish wave with max amplitude determined by the zener voltage. It should not have much of a negative component, since the zener would act a damper for negative spikes, so I would expect to feed this to the opto inputs.
If you're feeding the VR inputs then you would be relying on the negative spike(s) of the switching noise to trigger the zero crossing circuit. How much of a negative spike exists at the switched side of the coil depends mainly on how damping has been set up for your ignition drivers. If there's not much damping, then that negative spike could be pretty big, so you'd want a zener to clip that as well:
Do you have a scope so you can look as this input signal?
