Well I own both, and I can give you some of the differences that I notice. They may not be all technical though.
1. The 4.6 produces less torque and the band starts higher up.
2. The 4.6 is a smoother rev, and doesnt shake as much as the 5.0.
3. 5.0 has been in production forever and parts are easier and cheaper to find. Even bolt ons.
4. 4.6 is expensive to build due to it's relativly new production, and it's technology is different making parts cost more.
I Think you would be more happy with a 5.0, only because all of us who thought we would just use a few bolt ons ended up craving the mad power that require more then bolt ons. If I were you I would keep looking for a 5.0
Happy Hunting
-Kevin