Biggest difference will be going from a solid to the IRS in the rear. The 5.0 has torque down low...the 4.6 has to rev high. Doesn't wake up until over 4,000RPM's....but you can go to 6800RPM's now.
If you like the new body style, don't mind the IRS (better ride, but not as good for track duty) then go with a 99+.