One thing you'll need to change is the exhaust manifolds. MarkViiis have the driver's side cat welded right to the manifold, won't fit in the Mustang. Also you're either going to have to find some way to make the IMRCs work with a window switch, or delete them. Marks have a 6-bolt crank, so you might need to pick up a 6-bolt flexplate, or flywheel depending on whether you're going auto or manual.
You don't need the Cobra intake manifold, and the cams aren't different enough to do a cam swap IMHO.
But I guess it depends what your plans for the car are.....