You either have to buy a 03-04 Mach 1 hood and buy a factory Ford shaker to go with it, that option is pricey. I did it on my old 01 GT, it cost about 1500 after paint. Or find the CDC version that uses your stock hood, that one is alot cheaper, but I don't think it looks as good as the Mach 1 hood.
Do it right and get either one of those kits or don't do it at all. Cutting out the honey comb insert and hood isn't a good idea.