Factory 5.4 Shelby Charger On A 5.0

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I suppose it would be possible since the supercharger is a Eaton OEM product, but the casing itself might be different from the Roush, Ford Racing, and Saleen products. One Eaton's website they say they provide the internals and the aftermarket seller is responsible for the casing.
Q: Does Eaton make aftermarket supercharger kits?
Eaton only produces OEM (factory, from the dealer) type superchargers. The Eaton aftermarket business consists of 4 partner companies. These companies purchase certified components and internal sub-assemblies direct from Eaton (bearings, rotors, gears, and seals). These are the same internal components found in the Eaton OEM assemblies. The only difference is that each aftermarket partner company creates its own housing designs to fit the needs of the aftermarket applications. These housings are designed and tested in conjunction with Eaton to ensure proper specifications.
You're probably better off just getting a whole kit to install a supercharger.
I figured the same my self but considering you can pick up a take off charger from a Shelby with 10k on it for around $800 it would be nice to find away to make it work. I'm inclined enough to take care of the rest just the intake problem:/
There are no bolt-on kits for it. You would have to do a significant amount of fabrication to make a lower intake if you plan on the traditional mounting sense, especially if you were going to try to air/water cool it like in the OEM setup. Anything you save on the blower will quickly be spent in fabricating a one-off kit, not to mention dealing with the shortcomings of the OEM blower (there is a reason it's being sold), the less space between a 5.0's heads versus a 5.4L 4v's, etc.

In short, if you have to ask, you don't have the fabrication skills required to do something like this. Yes, it can be done.
Even if it does "work" it probably won't work for long. There is a reason the older modular blocks are still being used for the GT500. Put a blower like that onto the 5.0, particularly with its 11:1 compression ratio, and its only a matter of time.