Well, now I'm a little more confused than before.
Bolted everything back together and took the bike for a little spin.
Seems to be sitting at 14.1V now @ idle.
Same issue under throttle, voltage drops, but only to around 13.4V minimum this time.
Heres where it gets new.
At idle, when the fan comes on, voltage will only drop now to 13.7V (as opposed to 12.7V)... but ONLY if the brake lever is pulled. If I release, the fan will now run, and bike will idle fine at 14.1V.
So what on earth is going on here?