I used a spade bit with drill guide called a Portalign. I don't think
it's in production any more, but there are similar devices around,
such this one from Sears:

http://www.mysears.com/Craftsman-Drill-Guide-reviews

For using the dogs in the table with dogs on a moveable vice jaw, the
table holes should be spaced no farther apart than the vice travel.

Mine were 7/8" diameter. Some pictures he

http://bullfire.net/Bench/WP_Bench.html

I'm not sure I can help much with the mess the drilling will make.