Read the following:
http://autorepair.about.com/library/faqs/bl053c.htm
I prefer to use a drill bit mounted on the 1/4 in rod rather then the coat hanger mentioned. I drilled a hole in the bottom of the rod to the size of the bit and inserted the bit. Then I used a set screw to hold the bit in the rod. I turned the rod by hand and vacummed out the residue. The article talks about the total no of plugs and how to get them out and the replacement parts.
The horizontal runner may be plugged and that can be determined by back blowing from the holes you just cleaned towards the EGR valve or it could be the ports under the other 2 plugs. Remove the plugs and see if they are clear. If not clean them the same was as the others.
The only metal shaving will be from drilling and taping the plugs so you can remove them. A vacuum will clean up the shavings before you remove the plugs. There should be no metal shavings from cleaning out the ports into the intake manifold.