The important differences to know between the 4.6 and 5.0 are that the 4.6 doesn't respond as well to headers as the 5.0, you can go higher on the rear gear ratio with the 4.6, and the factory head/intake/cam package is better on the 4.6.
I'd start with an x-pipe/catback combo, then a CAI/TB/upper plenum combo, underdrive pulley, and then gears and a handheld tuner. Those are the basic bolt-ons to start off with. You don't necessarily have to go in that order, either, just make sure to do the gears and tuner at the same time to keep your speedo accurate.