The yellow cluster wires are the brake fluid warning lamp. Does your M/C have one or two sets of contacts for the float switch(es)? I recently swapped reservoirs on one of my 116s and the original one had two float switches but the new one had only only one. The extra pair of wires could cause a short or warning light flashing if they came in contact with earth, maybe that's why it was disconnected?
Or maybe just the float switch was dodgy and the wire was cut to stop the light randomly flashing? I would think removing the bulb would be easier though...
The black wire is related to the cluster backlight I think, but can't really tell if it's power or ground from that pic.
It's disconnection may be the cause of the PCB track damage, or whatever caused the PCB damage could have burnt out the ground wire
The missing wire from the plug is the high beam warning lamp. That could be related to the white wire tapped into the yellow loom wire - possibly someone did a dodgy high beam upgrade which overloaded the parker circuit? The cluster backlights are on the parker circuit, and the burnt tracks look like they're part of the dash dimmer circuit maybe?
What does that white wire connect to?