You probably need a programmer and custom tune. The 4.6 ECU doesn't work exactly right with a 5.4.

 

A tune is on the list, my wallet just needs to catch it's breath after the swap. I am amazed it runs as well as it does. Did a 60 mile freeway run yesterday and it runs great. This thread just made me aware of something I was puzzling over, the little stumbling on no load situations.
Mike