On mine I disconnected the flasher under the graveyard at the back of the machine and mounted a 555socket on top of the ramp facing the graveyard, it lights up when your bonus is being totaled (when you hear the lightning).

If your putting LEDs in certain areas, it's the resistors that govern whether you put to much voltage in and cook an LED. I bought a mix pack of single LEDs off eBay that came with a heap of resistors to choose from too. Used google and wired them into my G.I lighting in places like the rats hole and so forth.

No, but it's likely the LEDs won't turn on with half their specified voltage. Also, the 6.3V is AC, whereas LEDs typically only turn on in one direction. Your kit may have bidirectional LEDs or two mounted in opposite polarities though.

It tends to flash in alternating pattern with the other corner.

You can get 12V from the coin door interface board (J4, pins 1 and 4) in the cabinet or from the backbox (J116 or J117, pins 2 and 3). If you don't want it to be lit when the general illumination is off, then you will need to use a transistor, relay, or PIG2 (http://dkpinball.com/) to control it.