The 351W will bolt in place of the 302W.  Motor mounts and trans are the same.
Headers are available, but it's a tight fit and kind of a bear to work on.  The 8.8
diff will withstand a lot of power.  Engine weights are close enough to not be an issue.

But here are some other things to keep in mind:
-  Front accessory brackets are differant.
-  You'll need a bigger radiator.
-  You'll have to rework the suspension and brakes to handle the power.
-  The stock T5 has to go.  You'll need a TKO 500 or 600.
-  An auto trans will work great, but needs to be seriously beefed up.
-  Any intake big enough to feed 408 cubes at 6,500 rpm's won't fit under your hood.
-  Stock computer can be made to work with something like a Tweecer.
-  It won't pass emissions.
-  It would suck fuel like there's a hole in the tank.
-  It would be real fun to build.
-  It would be really cool to drive.

Have you considered a well built 347?  400+hp without a blower is fairly common.

A 408 stroker seems a bit ambitious unless you want to throw a lot of
money at the transmission (TKO) and the rear-end as well as the engine.
 A much easier/cheaper swap would be something like a marine 351w crate
engine which is almost a bolt-on affair and produces about 340-350hp out
of the box.  Throw a supercharger on that and you're up to 500hp-ish
(and probably back to doing the tranny and rear again).  The Mustangs
are quite cheap to do 300-400hp, but after that, things start to add up
quickly.

Cheers,

Same mounts and if you could get ahold of a Lightning lower intake manifold
and EEC that would be the way to go. NO the manifolds are NOT
interchangeable. The 351W is an inch wider. Just go to the local
Checker/Schucks/Kragen speed shop and look at them on the wall. You can tell
just by looking at them the 351 is wider than the 289/302.