Alternator from a 4.6L will NOT bolt up to a 5.0L's bracket. It's a 3g, but it's totally the wrong bolting arrangement.
Go hog-wild and squeeze the whole interior from the 99GT in there. I've seen it done on a '79 Fox, although I imagine some details like the front dash, rear seat, and wiring up the gauges could be a bit of a nightmare. Seats should pretty much just bolt right up, unless they're power seats - have to get fancy with the wiring there, too.
If nothing else ... the shift knob will screw right on there in a few seconds, no tools required.