Did you guys clean out your EGR nostrils while you were cleaning the intake? You have to remove the two hex plugs with the intake off and run cleaner + any thin probe you can get down there to clear a patch for the EGR gases. Looking past the throttle body, you'll notice the two smaller holes opposite the two bigger IAB holes. The intake manifold and his friend the EGR have been bad boys, they've been snorting coke. Black, carbonaceous coke. Pick out what you can. When you can get the carb cleaner to squirt through these holes from the other end, then good enough. The more coke you can clean out of there, the longer those nostrils will flow without plugging up because once you put it back together the EGR is going to be peddling his drugs to the intake again. Naughty intake! Snorting coke!
Rather than take your intake off to get to the lower hex plug, you can probably just take the end hex plug off and disconnect the EGR pipe for now and shoot Berrymans B-12 through the hex plug's hole (plug the EGR hole with your finger or something). Use something thin to probe the coke out and clear a path. Either remove the throttle body or open the butterfly and shine a flashlight so you can monitor the progress on the intake side. Probe what you can from that side. You might want place some shop towels inside the manifold on both sides of the notrils to mop up the B-12, otherwise you risk flooding your cylinders if too much gets in there and your car might be hard to start. Don't forget to remove the shop towels before you put things back together! Don't forget to put the hex plug back on, use a little teflon paste on the outmost few threads.
Also, if you need a more succinct description of how to clean these puppies, check out shotimes.com or do a search on shoforum for intake nostrils.
Rick