The biggest thing you'll need to do to a '96-'98 4.6 2V is do a PI (performance improved) intake manifold and heads swap. Those two parts are the bottleneck of these engines and you'll need to replace them with a '99+ 2V set-up if you'd like to see nice gains.

The engines will run forever and has tons of potential, but unfortunately, the stock manifold and heads are garbage from a performance stand point.