I assume it is unavoidable having some of the carbon soot fall down into the intake manifold while drilling out the port holes. How bad is it that this soot falls in? Will it be detramental to the engine if larger amouts make it in?

 

You shouldn't be using a drill to clean the holes...

I usually have a shop vac sucking in the carbon as I loosen it up with a screwdriver/body hook.