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.
