So far i have just done a custom intake, and i am redoing that this week since i have done more research and can fully custom make one from the turbo inlet, and im still trying to locate the correct Vacuum line for a boost gauge. i have also replaced the factory 9005 lightbulbs, with the Silverstar ZXE lightbulbs and have incredible success being that the headlights are projector style.
as far as the subwoofer goes, i did use the factory stereo, and it has worked fantastically in conjunction with the Auto-Volume and Equalizer. The only way i have seen any kind of factory subwoofer connections, is if you purchased the sun and sound package, which basically added bose speakers, and 2 6x9 subwoofers in the rear deck. which to me, adding a subwoofer was more worth it than the Bose system in my personal opinion. i can say because there is no replacement for after market head units, id recommend to use the factory headunit, and find a subwoofer like Kicker's Bass Stations. luckily, the subwoofer i purchased was simple to install, but not so easy to connect to the rear door speakers.