The 6v AC limiter in the treatland link, apparently a Yamaha unit, has only one wire. The case is the second wire. Mounting the case solidly to metal takes care of the ground connection. The one wire is attached to the power wire coming out of the stator anywhere along its way to the bulb. Seems to be a red wire on the diagram and pictures. Between the red wire and ground. Looks like the red wire can be accessed at the engine j-box or horn. That should protect the headlamp.
http://www.rexs-speedshop.com/XT250-XT500-TT600-Voltage-Regulator-6-Volt
I was WRONG about the yellow and blue floating output, I think. I've never seen an ET3 stator, and the diagram shows no ground on those two coils. Faded memory reminded me of the two coils wound together as one, with one end of each coil grounded. Two varnished ground wires under a screw and two colored wires coming out of the stator from what appears to be one coil. For the brake and tail to work from that diagram it looks like the two-in-one coil deal. Can anyone verify?
If so, that means THREE separate circuits (outputs/wires) with one end grounded. Sorry about that. Three voltage regulators?
Since I have never tried it, someone else can be the experimenter. You could attach the regulator underneath behind the brake/tail, possibly to a fixture stud/screw, and alternate attaching the regulator wire to the yellow or blue wire if one bulb blows. The engine J-box is another possible wire connection point.
I would try yellow first. It has more possible problem points. The blue brake light seems to have a single coil wire dedicated to a single bulb. Easiest to maintain and less sources of trouble. Good connections, good ground.
If a bulb still blows, it MIGHT be possible to connect the regulator wire to both the blue and yellow wires, but I know nothing about phasing between those two coils. Do so at your own risk. The limiter looks like an open switch, or looks to the stator like nothing is attached, until the voltage goes too high. The risk is small, due to the weak stator output. Be brave, and let everyone know if that works or ruins something.