If you haven't read it already, I have taken pictures of my 'modified' rods and posted pics in the following thread (scroll to near the bottom of the first page):-
http://forums.sv650.org/viewtopic.php?t=41526
Mine appear to have had the extra hole/s drilled as I have 6 'ports'.
I can't offer any advice as to if this is the better method though.
However at the end of the day if you want to increase flow, making a bigger pipe (drilling holes out) or adding an extra pipe (drilling additional holes) presuming the proportions are correct, will both effectively achieve the same thing. It is probably easier to enlarge holes rather than create new ones though?