Swapping a 1996 TekSkid 4.6 into a 2004 V6

This is definitely a little more advanced than bolt ons, as I don't believe your PCM will support a 4.6.

Challenges I can think of off the top of my head:
Motor mounts - I believe the 3.8 uses a small block mount, which is definitely different. This might require a K Member for the 4.6.
Gauges - The cluster from a 96 uses a mechanical Odometer, and a different speedometer signal. I think even the plugs are different. Unless you want to rewire the gauge cluster, you might be better off using the V6 gauges and getting a speedo from a 99-04 V8 car.
PCM - I seriously doubt the V6 PCM can be setup to run a V8. You will probably need a PCM from a 99-04 V8 car, as well as the wiring harnesses to go with. Swapping the PCM may give you issues with PATs though (my brother had this issue doing a 4.6 swap on a 98 V6 with a 97 PCM).
Wiring - You basically have two options here: get the wiring from a 99-04 V8 and adapt for the 96 engine (which likely means going to coil on plug), or using the 96 wiring and trying to adapt to whatever PCM.

It's enough of a job that you might come out cheaper/faster to sell the V6 and buy a GT to put this in. It's pretty straightforward when you have a compatible PCM, K-Member, Rear end and suspension already installed.