Hmmm ... several seemingly-relevant questions that haven't been asked ...
What year is your B40? Knowing whether it might originally have been 6V, and converted to 12V for the MicroDigital, or was originally 12V and has had some random switch fitted by a p.o.?
Is the "ignition switch" a proper one - marked "IGN" and has a spade-like 'key' that fits in a slot in the middle - not a Lighting switch (screw in the middle) that's been cobbled into place? And there's a separate Lighting 88SA switch?
It is fitted with 2 Boyer boxes one red micro digital and a black one.
Both are connected to the bike's electrics? The "black one" isn't also an ignition (if it's a Boyer-Bransden, would have a label showing "MicroMark" and a 3 or 4) and only one is actually connected?
If both boxes are connected, as posted by others, the "black one" is likely a B-B "Power Box" regulator/rectifier; any label or markings on it?
Off, on and emergency start if wired as standard,
On mine I get no spark in centre position. Both other positions seem to work the same.
Then that's at least part of what's wrong; on 12V, "emergency start" should've been disconnected. Essentially, the wiring diagram "kommando" posted shows just that, by what isn't
on it compared to the corresponding '6V' diagram ...
A 6V diagram would show the Green/Yellow alternator stator wire connected directly to Ignition Switch terminal 16 or 17 (i.e. not to the rectifier) and another Black/White wire from the coil "+" terminal to Ignition Switch terminal 15. A 6V diagram would also show a third contacts diagram under "IGNITION SWITCH", labelled "EMG." or similar.
Your bike clearly appears to have "EMG" wiring connections; if so, when you use the "EMG" setting, you're putting AC into the DC wiring; with proper electronics also connected to the DC wiring, they (the electronics) will be donald sooner rather than later. At least stop using the "EMG" setting 'til you can work out what dpo have/n't done.
The original alternator is not the strongest output even when in a 12V conversion
The original alternator (RM19) produces less
when regulated to 12V than when regulated to 6V - ~100W and ~120W respectively.