what exactly are your goals, if you are a little more specific someone may chime in and help. Usually a 4.6 to 5.4 swap isnt normally very cost effective in terms of HP per dollar. But Bill Fisher would be the one to talk to about the 5.4, he has done alot of work researching and experimenting himself on them.
what kind of advise do you need?
All i know is that you need a lightning lower intake with a cobra(pre03)upper intake. i think you can use your stock headers but if you want to go aftermarket you have to stay with shortys. And you will need the H or X pipe costom fabed.
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Do more research online