Will a 1997 4.6 engine fit in 1999 5.4?

No, a 1997 4.6L engine will not directly fit into a 1999 5.4L engine bay. While they might share some similar components, the 5.4L is a significantly larger engine, and the mounting points, accessories, and overall dimensions are different. You'd need extensive modifications, which would likely be more costly and complex than just replacing the 5.4L with another 5.4L or possibly a different engine altogether.