If I'm undertstanding this correctly, you'll have a TRD
exhaust, springs and short shifter with the car when you purchase it? If you don't mind me saying, the TRD
performance package is a rip off. Save yourself some money there by getting a GTS then buy the short shifter (45 min install anyone can do), the springs, and exhaust (bolt on job). You can easily do the short shifter and if you have any mechanical inclination at all the exhaust. Installing lower springs can be a pain from my understanding.
If you decide to go with the TRD
GTS, I'd suggest an Injen
Race Division CAI
(~$200US) first of all. Some nice light weight rims, if you're going for looks and performance, get 17s. I would not suggest a dual exhaust at all, you will lose too much back pressure, which is why I'm still not sure if I'd do new headers either. I'm not familiar with how the TRD
headers effect performance. A lightweight flywheel would help a bit, TRD
has a JDM one, but TOMs Lightweight Flywheel is even lighter (~$500US). Limited Slip Differential would definitely help your 0-60 time, too (~700 to 800US).
Basically, this is what I would do if I wanted a short 0-60 time, had a TRD
GTS and $2000US. Injen CAI
, TOMs flywheel (get the TRD
if you'd like to keep your warranty), front strut bar, limited slip differential and buy a round of beers for whoever helped you with the installs.