Both Zeners are still there, but I do have the Boyer black box (mounted near the battery) and the Zeners are still connected. Any reasoning for that? I assume since there is a black box, I can ditch the Zeners?
Depends what you mean by "black box"?
If it is a Boyer *Power Box* then you can safely remove the Zeners and 2MC (provided the box is the type with the internal capacitor?), as they should have been disconnected anyway, along with the standard rectifier, as a Power Box is a charge control box.
If the "black box" is a 'Micro-Mk3' box, then that is the electronic ignition amplifier box and has nothing to do with the charging circuit, so if you have an electronic ignition fitted then you will need two *boxes*, the charge control box doesn't necessarily have to be a Boyer type.