Green Wire & Battery question

Ok, so I can't remember if it was the green/yellow, green/white or solid green wire, but I found one of them had come out of it's old style bullet connector, which was plugged into a yellow wire with a double adaptor. I've soldered it back up anyhow. This was inside the battery compartment, the yellow wire is one of three(?) coming from the modern style regulator, the green/(Y)(W) wire disappears into the wiring harness. I've got a high output alternator, dual output single coil with Boyer ignition. The bike has been running but popping a bit no matter how I adjust the timing, and last night seemed to be cutting out for a micro-second off and on. Could the bike still run at all if one of these wires was disconnected? Perhaps it was still touching intermittantly?

Battery question: where do you normally run the battery vent hose? Right now I've just temporarilly stuck the tube into an old 35mm film case (remember those?!). My previous Commando was venting on my chainguard when I bought it, I re-routed it somewhere under the frame but I was young and stupid so it was probably blocked up with road grime or corroding the cradle underneath anyway.

The green striped wires go down to the alternator. One of them missing would inhibit the charging system. If the battery got below 10 volts or so the Boyer would change its timing, which could indeed cause popping.

I rout the battery vent hose down behind the primary chaincase.