Sparkplug, your warning light assimilator or charge warning light controller will generally only tell you that either the charging system or the battery voltage (depending on which method is used) is less than the required amount not more than and the Zener Diode is supposed to 'Bleed off' any excess charge and turn it into heat which is why it is bolted to the footrest plate in the case of Nortons, or else in that aluminium 'sunburst' heat-sink generally mounted under the lower triple clamp on Triumphs.
The boyer ignition you have fitted will not affect this, there is however a boyer charging controller that can be fitted as an aftermarket device this does away with the necesity for a separate rectifier, Zener diode and (depending on the model purchased) warning light assimilator. The best way to check what charging control system you have is to see whether you have a rectifier fitted and wired up. It is generally mounted under the seat on the frame plate above the battery tray. It looks like a stack of black thin washers with male spade connectors for the appropriate wires to attach to. If you have a rectifier connected then you also need a Zener diode connected, failure to connect it can result in overcharging, boiling the battery acid or even in extreme cases a burst battery which plays havoc with chrome and other parts.
Since you note that the red wire is still attached to the footrest plate It may well be that the male spade-connector on your zener diode has broken off and is still attached to the wire in the female end or else lost.
The Zener diode on Nortons looks like a large dome-headed bolt with a connector tab sticking up out of it that the wire you are refering to is connected to. This diode is bolted through the footrest plate from the inside, it secures the red earth wire and is itself mounted with a small nut on the outside of the plate. A new zener diode can be purchased quite cheaply from any of the regular British bike suppliers mentioned on this forum. BSA, Triumph and norton all use the same system and part.
Good luck