Can a 1997 Ford f150 motor fit into a 1999 Ford f150

Reasonably - no.

In a nutshell, You'll be swapping the trans, exhaust manifolds, etc. along with it. The motor itself of course will fit, but you'll need a 4r70 trans. (5.4 has 4r100), and the manifolds along with the front section of the exhaust are different. Then, there's the computer........