???s on a 01 4.6 swap into a 96 gt

For a plug and play swap, re-use the wiring/ignition/PCM/fuel from the original car. Otherwise be prepared to re-design the electronics.

If you prefer to go with COP style ignition, there are aftermarket plug and play harnesses available. I recall seeing someone "advertising" on this forum.

Here's an example.
http://www.modularfords.com/forums/showthread.php/168019-Plug-and-Play-COP-Conversion-Harnesses!!

Other differences that come quickly to mind are the design of the engine valley heater return, Front acc belt routing (may have to swap idler pulleys and belt tensioner), oil pan level sensor.

There's needs to be a sticky/FAQ entry for this topic if there's not already one around.

I just put in a 2004 PI engine complete from throttle body to oil pan. Starting from the bottom up, I used the 2004 starter that came with the engine. I believe it was a two prong and the ground needed to be changed. I can't remember exactly, but this shouldn't be an issue if you reuse your old style.

The engine mounts are obviously the same, but I slapped some energy suspension mounts with poly material and so far I love them. Very quiet and the motor doesn't twist as much.

I used the front accessory cover from the 2004 engine and all of the new accessories. My old NPI engine had 235,000 miles on it so, I didn't want to reuse anything. I kept the spark plug wires and ditched the coil on plugs. The coil packs were modified to fit the front cover and sit very level. I will have some pictures soon. The intake manifold was drilled and tapped at the aluminum crossover for the second coolant port. Pretty easy.

I reused my fuel rail as well because of our return style fuel setup. Basically reroute all of your wiring and use the 1996 stuff. That's what I did and it works great.

have you considered doing a PI swap (heads) on your NPI. The 99+ heads have smaller combustion chambers and Improved airflow resulting in more hp than a 99+ PI motor. here's a link I found on some who has done this(sorry it was from another site). PI Swap Write-Up, 1996 Mustang GT - Ford Mustang Forums. You have all the parts with the 01 motor.