All cobras 96(maybe 94-95) and newer use the 4.6 281 V-8. There is no ford 5.0 anymore. Even the concept cobra uses the 4.6 with a blower on it. My friend has a 98 Cobra with a 144 and the 4.6 in it and the figures look almost the same on a dyno to the new cobras.
I dont believe there is a 5.4 in the 2000 cobras, at least not from the factory. But I'm not a ford guy, I just know my friend loves his cobra and thats how I found out the info.
Try using smaller injectors if your running so rich.