If it were MY car, so feel free to disagree, with $3,500.00 I would probably get a drop-in air filter, a decent muffler just to change up the sound a little, minor cosmetics like matte or gloss black items to replace all the chrome things and painted reflectors (I said kidney grilles I meant reflectors), some Eibach springs since they're conservative and comfortable, and a decent set of wheels, there's always some great deals on used wheels on this forum.
Would make for a simple, clean, nice daily car that would be good fun around town on the weekends. Just be patient and check the buy/sell sections of this forum often, there's no reason to rush your mods all at once, you have all the time in the world.
But for pure power route, a tune would be good, and maybe a primary cat delete? Get the Turner test pipes, they keep the secondary cats and the resonators, and simply replace primary cats on your stock pipe, so it won't be all that much louder and won't really be smelly. You can also get the Akrapovic CEL Delete-R if you don't want a tune.
Heck, just test pipe and Delete-R for the CEL would get you much more power than just a muffler, and be 1/4 of your budget.