zulu beat me to it. I was going to ask about the rotors too. since you were metal to metal the rotors deff have a groove in them. Id be willing to bet you can feel the bump in the rotor with your finger and the new pads dont fit in the groove that the OEM pad created.

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2002 4.6is Dinan S2
Titanium Silver/Black Alcantara

DINAN
Stage 4 Engine Software
Automatic Transmission Software
High FlowThrottle Body
Free Flow Exhaust
Cold Air Intake System
High Flow Air Mass Meter
OTHER
CCFL Angel Eyes
Stealth XM Radio in ashtray : FM Mod
Pilot H3 Fog Bulbs
Cleared Headlights: Hi/Lo Beams
Hardwired Radar Detector
IN PROGRESS
Powerstop C/D Rotors: (on backorder)
W/EBC Red Stuff (F)
W/Axxis Deluxe (R)
Dice Ipod: Aux Input for XM
THINKING
SMG II
MK4
Bluetooth