Yeah... they're pretty well a bolt in. There are only very minor mods that are needed.
I have one. Just did the very first baseline dyno run yesterday. It's running hella rich and needs more timing but you can see the potential. NA 4.6's just can't expect numbers like that.
Why hasn't it been done more? Because the aftermarket wants the things that will sell well. People only care about peak numbers so the parts makers only make things that get huge peak gains. If people knew more about performance they'd be going for area under the curves which is where the 5.4 shines. It's a tight fit but it does in fact fit just fine.
I'm about to head down to get the first set of longtubes made and those should come to market pretty soon. I've already worked out the intake design with HPS and they're bringing the new 5.4 specific intake to market really soon here. Other than that, you'll want ported heads and nice cams to take advantage of the extra cubes. Longtubes seem to be worth about 30rwhp or so with a nicely cammed motor so I'd plan on including a set in your build up.
FWIW, my numbers look kinda low but I gotta tell you, the actual performance is tire shredding and a lot of fun. Can't wait to put a better tune on it and run it again.