It is worth it. Use a 96-04 Mustang K-frame. If it's going into a Fox, you must modify the right and left mount tabs on the back of the K-frame, but it's doable. You also need to go hydroboost, or manual brakes. A booster will not fit with any modular engine. You're on your own with wiring it up. You'll also have to do something about the intake. The truck intakes are TALL!! You can go with a customer intake or a 4.6L intake and get the adapter plates they make.
I've done 1 4.6L swap and I'm currently doing another. I've done them using Mustang donor cars, using the whole wiring harness. Since 5.4L's didn't come in Mustangs you are going to have to figure out something with the wiring. It can be done. Maybe a painless wiring kit, but that will still be a pain in the ass.
FI on a 5.4 2v is fine. N/A is worthless. you need forged rods to handle any real power though. they WILL blow out above ~5000rpms and 10 psi. if you keep the boost low and the rpms low it will do fine. 8 psi and less than 5000.