I used 1/2" pvc and a 1/2" masonary drill bit to drill the rocks. It was really easy. If you keep the rocks fairly moist I wouldn't worry to much about die off. Drilling is really quick. You could drill a rock in about 10 seconds and then put it back in salt water. You could also stack the rocks on underwater.
Check out this thread if you want more info on building pillars
http://www.reefcentral.com/forums/sh...d.php?t=746318