The rear elbow that you drilled out is now probably out of spec. It has a fixed orifice of a calibrated size which is supposed to meter (limit) the amount of crankcase vapors drawn out of the engine. The orifice can be cleaned out by pushing the end of a paper clip through it, but it is not supposed to be drilled out by a drill bit larger than the orifice size. Get a replacement from the dealership, get new grommets for where the elbows enter the valve cover, and replace any old rubber tubing that may be hard and cracked. None of this is very expensive.
2001 WJ Limited with Quadra-Drive, Kenne Bell Supercharger, 3-inch Kolak exhaust, Stillen rotors (F/R) and MM pads, Addco sway bars (F/R).