Will a top mounted factory supercharger from a f150 4x4 5.4l v8 work in a 1999 Mustang Cobra?

I agree with rick, the intake will be different. But I'll add a few things. If the supercharger is from Ford Racing you may be able to get the rest of the pieces you need separately by checking out the part numbers.

Ford Racing has a couple of choices for superchargers but they are all for 2005 and newer engines. If I remember correctly, they have two that fit the 4.6 and made around 400 hp and two others for the svt cobra that cranked out 630 hp. The other issue is that to get the most out of it, you'll need a fuel calibration mapping and not totally sure, but possibly larger injectors.

Mustang superchargers ran off the stock manifold, while f150 units had different intakes on complete units. If it's an aftermarket one, I'd check out the manufacturer's website and see what's in one of their kits.

there was no factory supercharger for a 4x4 f150. Only the lightning had it and that is 2wd.