I assume the head was re-decked when it was ported and polished? First thing I would do is reset your ECU by disconnecting the negative battery terminal for a few and depressing the brake pedal a few times. Still no change I would check the compression (should be higher since it has been re-decked) Make sure all the vacuum and boost lines are connected and not leaking. My boost was low and it was making a fluttering noise and I found it to be the up-pipe gasket that connected it to the cross-over pipe. I have heard of the aftermarket intakes making it idle rough until the computer "learns" the change, thus the ECU reset. Someone once told me that if you port and polish a head in the wrong spots then you can actually screw up a head even worse because you mess with the flow angles and stuff like that but I am not to sure about that. Hope this gives ya somewhere to start....

Good Luck

 

Oh, I forgot, the CEL will get thrown with no Cats so I would have that pulled at Autozone to verify Catalytic Efficiency Code, or whatever else it may be.

 

check your hoses