There is probably a better way, but I use the following script run from my 
.xsession file.  This works for almost everything except for Chrome.  For 
Chrome the scrolling is still non-natural.
 

Script XFixMouse.sh
---------------------
#!/bin/sh

#ID     Button
#-------------------------
#1      Left click
#2      Middle click
#3      Right click
#4      Wheel up
#5      Wheel down
#6      Wheel left
#7      Wheel right
#8      Thumb1
#9      Thumb2
#10     ExtBt7
#11     ExtBt8

DEV=`xinput --list | grep wsmouse0 | sed -r 's/.*id=([0-9]+).*/\1/'`
if [ ! -z $DEV ]; then
        # swap right and left mouse buttons and change scrolling to "natural"
        xinput set-button-map $DEV 3 2 1 5 4 6 7 8 9 10 11 12
fi

--------------------

Regards

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