s281 - Actually the engines in 01+ have a bit more compression and tend to run just a tick quicker...
compression does not make the cars faster and they also went to a different trans here is the stats.
1999 4.6 SOHC 260HP Mustang Engine
Throttle body: 66.8mm (2.630 inches)
Intake manifold: composite, cast No. XR3E-DC
Cylinder heads: cast No. RFXL3-CZOD
Combustion chambers: 42.40cc
Valves: 1.752/1.417 inches
Rockers: roller type, w/1.80:1 ratio
Camshaft lift: .505/.534-inch lift
Compression ratio: 9.30:1
Pistons: hypereutectic w/.188-inch dish
2001 4.6 SOHC 260HP Mustang Engine
Throttle body: 65mm (2.560 inches)
Intake manifold: composite, cast No. 1L2E-DL
Cylinder heads: cast No. RF1L2E-6090-D22D (or D24D)
Combustion chambers: 42.45cc
Valves: 1.752/1.417 inches
Rockers: roller type, w/1.81:1 ratio
Camshaft lift: .505/.534-inch lift
Compression ratio: 9.74:1
Pistons: hypereutectic w/.145-inch dish