The voltage selection block is USUALLY:
100V Violet (May have faded to pink by now perhaps? - unlikely though)
120V Yellow (May have faded to white by now perhaps? - unlikely though)
220V Blue
240V Brown
With some variation for the different power bricks in different games. If your using brown, then you're using 240V which is correct so leave the voltage selection plug as it is.
I don't have a missile command, I'm 100% going from reading the schematics but basically, if your monitor and marquee are lighting up then the input side of your transformer is fine (as we'd expect).
So, with that in mind, measure the 6.3V. This is AC so make sure the meter is set to an appropriate AC range. According to the schematics, pins 11 & 12 of the molex are, as has already been said the 6.3V for the coin door lights. Ignore whether they're lit up (the bulbs may be blown or missing for all we know!). The schematics show the two wires as "BU" - that could mean blue but without the cab in front of me I couldn't say for sure.
Those two wires come straight from the transformer windings to the molex with nothing in between. No fuses or anything. So measure them again. If you're getting no voltage then sorry, but either the wires are broken or your transformer is! It's rare quite frankly, but I guess it can certainly happen.
Since from what everyone is saying about the colours of the voltage selection plugs, it does sound like it's not the original power brick. But I really couldn't say on that as I don't know all possibilities of what Atari chucked out of their factory back in the day!