Hi Arya,
Yes, you are right around the corner from me. We've modified more than 40 GTs.... so you might say we have some experience on the topic. I PM'd you my cell phone. Give me a call and we can chat.
I know exactly what you mean about taking a car and modifying it and ending up with something that is somehow less than where you started. With the quality of components and tunes (largely because of this forum and the great people and tuners), we don't have this problem at all with the GT. Really, the biggest decision you will make is on the exhaust - to make sure that you select the set-up with the right loudness and quality to match your preferences. We've done about every exhaust set-up possible and I'd be happy to share my opinions and can point you to some nearby owners for getting their feedback when you narrow the field.
As others have said, the exhaust systems available are mostly cat-back and will have NO adverse effect on check-engine lights, driveability, or smog tests procedures.
Beyond exhausts, the GT is still a wonderful and unique car to modify - again mostly due to the well-known ECU architecture (thank-you Mustang owners) and the skills of the people in this community. If you go with something like a pulley & tune for a quick 80-100HP adder at the wheels, I can assure you that we have done this countless times and the driveability of the car is identical to stock. Starting, idling, driving in slow traffic, etc. are all impeccable. The only difference is the additional push of your torso into the seat when you use the go-pedal. The same can be said as well of the Whipple. The Whipple "whirs" just a tad louder than OEM at idle - some find this desireable, but the driveability is the same as OEM.... except for the aforementioned push of the torso!
Regarding CA Smog, the pulley upgrades aren't specifically exempted, but they cannot be discerned from stock and they have absolutely no effect on the tune in closed-loop ECU mode (the basis of the entire CA smog test). As such, a pulley upgrade will not adversely effect a CA smog test. The Whipple has been CARB certified by Whipple - at no small expense of time and trouble, and kits come with the appropriate EO sticker to be applied to the car.