Swapping a 1996 TekSkid 4.6 into a 2004 V6

Hey guys, as the title says, I’m considering swapping a 1996 Cobra engine with its matching harness, T56 transmission, gauge cluster, rad and fans, and stock exhaust manifolds into my current car, a 2004 3.8L with the T5. I will also be swapping my 7.5 to an 8.8. I was wondering if anyone has any input into this swap, such as reasons it may not work or things I would have to look out for. I’m hoping the motor mounts would match right up but I don’t know. They are 8 years apart and I haven’t bought the Cobra setup yet. I’ve also never done a motor swap before but I’ve done some basic bolt ons and maintenance with my other vehicles. Thanks for reading and advising! Have a good day!
 
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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.
 
K member needs to be swapped, and a t5 won't bolt up to a mod motor, you'll need a t-45 or t-3650 or another trans.

Wiring changed dramatically in 1999 so ideally you want a full 1998 cobra wiring harness, PCM, and guage cluster as well.

Ideally...you need a cobra donor car