If it were me, I would close up the extra holes in the valve cover and insert a filtered vent where the old draft tube hole that is plugged. The other possibility is to put a PCV valve where the draft tube was and put one filtered filler cap on the valve cover, closing up the other holes.
On my truck I blocked the side tube inside the draft tube and installed the PCV valve on the top of that tube. I installed a filtered vented oil cap and I will be closing up the slots on the valve cover.
