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OK, the way I read this, you installed an intake on an 06. The intake and instuctions were for an AP1/AP2 (not 06).
Well you missed something. There is an air intake sensor on the intake hose. This needs to be installed into the hole you cap'ed off. To install, put a few O-Rings on if and stuff it in the hole you cap'ed. This should take care of the problem
Also, next time you have a CEL, get the number. It is really the only way to be sure what the problem and solution are. That is why they have codes