What do I upgrade to get the most hp gain out of my 06 mustang gt?

Just got the new car i've already installed the ford racing cold air intake, now what do I do?

My plan is to do this in order
cai
Headers
Tune
Supercharger/tires
Tune
Suspension
Then body work

I want at least 400hp to the wheels then ill be done with it (for now)

Most likely you never will reach 400 hp, you don't even list what engine you have now.

It runs on the Ford Racing intake without flashing the computer tune? If so the air intake isn't doing you much good. I have a C&L intake on my 06 and it won't even run without the tuner reflashing the computer. With the intake, tuner and Borla exhaust it added 50 HP. I'd be careful about adding a supercharger unless your engine is very tight mechanically.

Have you ever heard of water/alcohol injection? SNOW makes a wonderful kit for about 600.00 dollars.
IT'S NICKNAME IS POOR MANS NITROUS!
summitracing.com
search for water injection.
at the snow website is a calculator for how much power gain is to be expected. There are systems that can give you 30 to 40 percent horsepower improvements.