If I remove the 5th and 6th port sleeves and actuators, will it affect emissions? I still have to pass smog here in Cali, but am considering pulling the 5th and 6th ports just to see how I like it.

 

Minutely.

 

yes, they will radically effect emissions as the emissons tests are at 15 mph and 25 mph in CA, and normally the ports would not be open limiting your intake timing to 50*. With no ports the intake timing would jump to 70*

Toss in the normal power loss down under 4000 RPM with no working aux ports, and it more than likely is a bad choice to remove them even without considering emissions.