You'll need the Eaton M112 specifically off the 03/04 Cobra to work with the adapter set up Nathan makes. It uses the air intake tube, MAF, throttle body, inlet plenum, compressor and 39 lb fuel injectors. The boxed upper intake is custom made. There are also gaskets, hardware, fuel pump etc to install. Nathan's kit includes everything but the tune you'll need and a cowl hood. It's best to get a dyno tune from a good shop, but we worked with VMP to get a good base line mail order tune so you can drive the car without worry.
Here's a link to that used kit I mentioned. It's the best used kit out there, and you can't beat the price ($2000). The only thing that has changed about that boxed upper intake since I made it is someone notched it to fit around one of the front coolant lines. On my car, I re-routed the line for more room. That kit put down over 300 hp on my car and on Richard's car (the original customer). Richard sold it to the guy who is currently selling.
http://3.7mustang.com/vb/f25/fs-99-04-v6-m112-kit-264473/