The pinout on the wiring harness changed sometime in 2003. It is a very easy fix, all you need is a small screwdriver or pick, electronic repair size.
You may also have adaptive brake lighting if you are 03+. (Brakes get brighter under panic stop). This will cause the LEDs to flicker. You can either buy a capacitor that clips onto the wiring or make one yourself. It is very straight toward.
Here is a pin out link
http://www.xoutpost.com/863406-post50.html