Engine Specs:
1990 5.o HO: 255 HP 300 lb/ft
1999 5.0 GT40: 215HP 288 lb/ft
2001 5.4 2V: 260HP 350 lb/ft
The specs on the GT40 might be wrong, but my research shows that was the rating of the Merc in 1999. Both of these engines will work just fine in the SN95 platform. You could go the 5.0 route as that engine fits in the body style as it was factory equipped in the 94/95 GT, however I'm not sure how the 4.6 ECM will work with the 5.0. The fuel injector plugs and plug wires would work. The firing order is also the same. I think it would work just fine!
The 5.4 will need a 4.6 oil pan and pickup, but other than that it is pretty much straight forward. The 2001 engine was a coil on plug engine, but I don't see why you couldn't use the coil packs and plug wires. The exhaust will be tight and will most likely require a customer fabbed H or X pipe. I had to use a Cobra driver's side exhaust manifold on my 5.4 DOHC, but I think you can use the Mustang exhaust manifolds on the 5.4 2V without any clearance issues with the steering shaft.
IMO I would go the 5.0 route. Speed parts are a lot more affordable and available. You can build a much higher performing 5.0 versus a 5.4. The Lightning 5.4 is the exception here though. If you were able to track down the intake and supercharger from a Lightning and put it on your 5.4 then I would really go that route, however I have not seen any hoods that clearance the setup and you end up with a Mad Max look.
Whatever direction you choose, keep us posted and good luck!