Hello, first, whining is likely coming from a pulley or component on the accessory drive. The power steering pump, alternator, tensioner pulley, idler pulley, air conditioning compressor are all potential culprits here. By removing the drive belt, you can spin pulleys and check for resistance or noise and try to isolate. A set of engine ears will help determine the source also.
As far as engine performance, I don't know what you mean about saying you replaced "all spark plugs and wires" -- this car has 8 coils -- for the coil on plug ignition system. There are no "wires" to change.
Have you replaced all 8 coil boots or coils with original equipment Motorcraft / Ford parts? This is essential. Aftermarket coils have a high rate of failure and misfire.
Beyond this, testing must be performed first hand using a Ford equivalent diagnostic tool. A power balance test and relative compression test would be helpful to determine what cylinders are not firing properly especially under load. You could also have a fuel or air system problem, but this can be discovered first hand.
