Stock for stock, showroom for showroom, all 4.6L are faster than a stock 5.0 HO. The newer they are, the harder they beat the stock 5.0L.
However, the '96-'98 are a drivers race with them. The '98s are actually very slightly faster. I have did a test with each one stock from a 5 mph roll to eliminate the launch factor. The '98 started pulling instantly.
I have no problems with torque in either of the 4.6L I have owned or drove. It makes the same torque 100 RPM higher.
The 4.6L is very comparable to a 5.0L as far as the top-end, except for some of head bolt torquing, in car. The camshafts are easy, if you have did it once before.
I have did a h/c/i swap on both a 5.0 and 4.6. It is all in what you are used to. I think they both have their place