Hey HaMaNy,
Here's my 2 cents.
1. K&N Intake System (the best HP gain)
Performance gains will be similar among the brands (which in reality will be minimal). Just chose one that is enclosed from the engine bay. One of the popular ones on this forum is Volant, and I am sure there will be a lot of input on this. IMO a higher flow drop-in and change the intake pipe (AirRaid MIT) is all that is needed.
2. Diablo Programmer (more HP + Fuel Economy)
Go with Black Bear (site sponser) as they have shown the best gains and customer service. They can do a specific tune on engine and transmission parameters, and also provide updates if more mods are added.
3. Lowering Kit (need the best brand)
Other will chime in, I went up

.
4. Magnaflow Exhaust System (for the lowest noise)
This is subjective. Are you talking about a catback or just muffler? I have the Magnaflow muffler and removed the resonator. There is a little drone and it is pretty loud (not obnoxious), but I like it. I suggest you look into the Corsa Touring since you want the lowest noise.
5. "Looking for headers" (need some opinions for the brand)
Since you are upgrading the intake and exhaust, addition of headers are ok but your tune will need to be tailored to the mods. In the end, do not expect more fuel economy with these mods because you will get addicted to the sound. You wanted it quiet right?
Good luck and keep us posted. Oh yeah, welcome to the forum.