Are you sure that the stock ECU can't handle what you want to do? I'm no expert but I've heard that our ECU's are plenty capable. A return style fuel system (probably custom) would definitely be needed. I'm not sure if anyone has actually maxed out the Duratec ignition system or found it to not be up to par to their build. I would talk to the people mentioned below....
Who is doing your tuning? Have you talked to Tom @Focus Power or Randy @FSwerks? Or you could even call Ray @McNews Automotive in Dilsburg, PA.
2012 Fusion SE 3.0L V6
'86 XR4Ti ; 2.3L Turbo, 15psi
1988 F150 Custom
'07 ST ; formally bewst'd - R.I.P
D23 Crew: #07