well man i dont know what to tell ya, you chose the auto for the conveinence, which is understandable, but then you have to accept the auto for its inherent crappy accelleration.
Your pretty much screwed from the start because the D series isnt gonna pull your ass to highway speeds at any amazing rate even after intake, header and exhaust. That being said, your best bet to make it move is gonna be boost. Sence your in the lovly state of cali, purchase the 5th gen civic kit from Greddy, it will bolt right up, then when you get your intercooler and charge pipes youll cut those to fit.
Problem is Honda automatic transmissions well, they kinda suck and if you go boost, then youd better be prepared to replace it. Also your not gonna get the most efficiancy out of the turbo because your not gonna be able to spool it right with an auto.
Your best bet is just to mash the gas and hope that semi is feeling generous