Personally I wouldn't use that efi setup, its going to be speed density efi and doesn't like many mods. you could get a mass air setup from a mustang and have a far cleaner install in my opinion. great motor though, I wouldn't go punching it out unless its necessary. upping the compression though will help improve power.
You'll need the throttle cable and bracket from a Lightning as well. If you plan on keeping the EGR, then you'll need the EGR spacer and valve from a Lightning. You'll also need to plumb the coolant through the spacer, from the back of the lower intake to the radiator filler neck.
When you get ready to put this combo in you're F-100, I'd recommend using an aftermarket EFI system for the engine and a stand alone transmission controller.