O My!
Ok first the "green plugs w/ the broken nipples." Those are the BVSV for the the EGR and the EVAP. the left one connects to the EGR, the right to the EVAP siystem. having either of those broken will cause a CEL
When you changed your plugs, did you change them one at a time? or simultaneously. Did you also change the Spark plug wires and the distributor cap and rotor?
If you also changed the spark plug wires and distributor cap, there's a good chance you changed the firing order.
You mentioned you disassembled the Intake manifold. Did you use the old gasket, or did you replace it with a new one. If you changed out ur gasket, you may not have completely removed the old gasket causing a vacuum leak in the system:
http://www.youtube.com/watch?v=2pU50nAwJmw
*TURN DOWN YOUR SPEAKER VOLUME; VIDEO IS LOUD*
That's what happened after i did my spark plugs. Is that similar to what's happening to you?