Does anyone know why the RT3 has two holes drilled in the headlight bucket? The first one is for the High Beam but not sure what the second one is for.
I expect Yamaha used the same bucket for many models.

My guess is the speed warning lamp that became mandated in Japan about that time.  I don't know if any other countries got it?  

"My guess is the speed warning lamp that became mandated in Japan about that time."

Yes, I agree with Mark.

A handful of Japanese Domestic Market (JDM) bikes were brought back to the US by returning servicemen and, as they got sold on to new owners, that red light caused lots of confusion!

Just out of interest, I bought a set of JDM TX500 clocks which have that red light in the centre of the bracket and, when I get the time, I want to sort the wiring out then spin the speedo up with a drill, to see if the light still works. As well as the red light, there is also a red line on the speedo at 80kph.

It's not just the RT3. Many Yamaha enduro's have 2 holes with a rubber plug in the lower one. Including my 68 DT1 250, 69 CT175 and 70 RT1 360 and many more bikes that i have owned like the 69,70 and 71 DT250's. Odd enough my 69 AT1 doesn't have 2 holes. Only one for the high beam indicator. Go figure!  

I wonder if the AT1 was considered not capable of exceeding 80kph, and so no need for the warning light?