Hmm, some clarifications:

This part you should do as root:
At the top of /etc/X11/XFConfig-4 there's a following section:
Section "ServerLayout"
Identifier "XFree86 Configured"
Screen 0 "Screen0" 0 0
InputDevice "Keyboard0" "CoreKeyboard"
# PS/2 Mouse using /dev/input/mice in Kernel 2.6
# Serial Mouse not detected
# InputDevice "USB Mouse" "CorePointer"
InputDevice "PS/2 Mouse" "CorePointer" THIS is your mouse
EndSection

A bit further down you'll find the corresponding section to your mouse which I posted.
If you had "USB Mouse" at the top, that's what you want to modify.


This part you should do as user:
Open an editor and type the following lines:
echo '#!/bin/sh
xmodmap -e "pointer = 1 2 3 6 7 4 5"' >/tmp/x$$
chmod a+x /tmp/x$$
xterm -bg black -fg white -fn 9x15 -name "Pointer Remap" -e /tmp/x$$
rm -f /tmp/x$$

Save the file as /home/your_username/.kde/Autostart/some_filename.sh
Then do: chmod 700 /home/your_username/.kde/Autostart/some_filename.sh
Restart the xserver with Ctrl-Alt-Backspace to test it.
If you use something else than KDE you can add it to the end of ~/.xsession but put a echo '#!/bin/sh before the xmodmap line.