Apparently a 5.4L 2V is a 99% drop in if the car was a 4.6l 2V. I have not done the swap but I've read enough threads on it when I was looking at doing one myself with TFS heads. Convert your v6 just like you were doing a 4.6L and then its apparently a few exhaust mods and the 4.6L computer runs the 5.4 ok.
Personally I'd just sell your V6 and buy a GT and mod that if its feasible.
2000 Mustang GT Steeda build #48. Bolt ons, suspension, Novi 2000.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.