ok. well since you have a 02 vert, your fuel rail options and spark options are better then mine. i will start on the basics of what you need and then later i can get into detail on the things you need to get and do to make it work.
intake: you can use the Boss 302 intake and the ap-08 is for a 351 not a 5.4. there arent any plates to make this work. what you will have to do is little by little sand down each side of the intake where all 8 of the injectors sit ( you will see when you get the intake on a navi longblock) personally i sanded and smoothed about 1/8"-3/16" off both sides. i suggest for the best fit is measure, with some calipers, the original amount between the far edge of the intake gasket and the end of the intake as descibed above. then make sure to sand the same amount at all 8 injectors. next, with a steel burr and sanding bits to finish off, i marked the center of the ports and made a line straight up from it on the inside of the heads (where the intake doesnt fit. that is what the sanding is for), then i measured my desired width on how much i wanted to grind of and ground away. do this in small steps and try to grind of an even amount every time. once you get your engine and intake you will know exactly what to grind off and how much you want. after i got it to fit, i drilled and tapped mounting holes once i got the intake where i wanted. a center punch will ensure the accuracy of the alignment of the bolt holes. take your time when doing this. you can use just the four corner holes if you do it right for a temporary fix or you can strip down the heads, take them to a welder and have them weld in 1/4"-1/2" plates in between the ports where there is no material for the new bolt holes. that would be the best way to do it if you know a good welder. thats whats needed to physically mount the Boss 302 intake to a navi longblock.
CAI: you will need to find your own way to mount a custom or modified CAI
exhaust: i just used factory cobra manifolds. you will not be able to use the navi manifolds. i have an off-road h-pipe and it came as a 2 piece midpipe. i had to bolt them on 1 side at a time. i also had to "massage" a couple small areas where the manifold flange hits the inside of the shock tower.
fuel: you can re-use your fuel system. your mustang uses a return-less style fuel system so you should be able to just extend a couple of fuel lines and use cobra fuel rails. since i used a return style, you will have to research that yourself. i saw someone using 05 f150 fuel rails and it bolted right down with minor modifications.
spark: you are lucky, all you need to do is reverse the polarity on your COPs or use the navi's COPs and might have to extend at the harness
wiring: lucky, again. use all your wiring and ecu. you just need to extend a couple of your sensors and everything will plug right up. for me, i extended my tps, iat, and both ect sensors.
cooling: this is the fun part. if you can get everything off of a 96-01 cobra. you will need the thermostat housing and all associated hoses, a coolant crossover tube (which needs to be extended a few inches) and this little pipe that comes out of the rear passenger side head freeze plug and re-using your heater core hoses, connects to that. i could only find this at a Ford dealership
minor things: bigger injectors, new polyurethane motor mounts, 11" 8 bolt flywheel and clutch kit, throttle body (many options), gasket set and any bolts and hardware you want to update (highly suggested) etc
thats the basics for now. i know you have some more questions. feel free to ask