Im running a D16Y8 manual 00' civic. Just trying to figure out which header and exhaust to get that is best for my car.

 

in my opinion i would leave the stock exhaust, you are not running a huge amt of horsepower to where you have to change yor exhaust, plus you will lose torque, and thats a no no with our cars.
as for a header go 4-2-1 it will give you more torque than a 4-1.
just do your research, find what you like and what you feel is going to get you to your goals.