Happy Days - Got it all to work, and learnt a load about linux - BONUS!
I now have two icons on the desktop (one to set the AB keys to left and right mouse / and one to restore the AB functions back so that the emulators all work) All this is done without rebooting -
Credit to ricki (xmodmap command) and urjman (thread and xkbset file)
Steps
1) Download the file xkbset from http://urjaman.dyndns.info/xkbset and save in your home directory (in your username is ABC then save in ABC [/home/ABC] ..EDIT - Ensure this can execute ie (chmod 777 xkbset)
2) Open the file browser and make two copies of .pndXmodmap (named .pndXmodmapb and .pndXmodmapnb) - If you cannot see .pndXmodmap go to view on the file menu and tick view hidden files
3) Open up .pndXmodmapb using file browser (just double-click - opens up in mousepad I think?)
Add the following two lines at the end
keycode 110 = Pointer_Button1 NoSymbol Pointer_Button1
keycode 115 = Pointer_Button3 NoSymbol Pointer_Button3
Save
4) Open up .pndXmodmapnb using file browser (just double-click - opens up in mousepad I think?)
Add the following two lines at the end
keycode 110 = Home NoSymbol Home
keycode 115 = End NoSymbol End
Save
5) Now open up a terminal window (System - terminal)
type cat > abmouse
#!/bin/sh
./xkbset m
./xkbset exp =m
xmodmap .pndXmodmapb
[Ctrl-d] <--- Dont type this actual press Ctrl-d
6) in the terminal window, type
chmod 777 abmouse
7) in the terminal window type (Remember - replace ABC with your username) - This creates the symbolic link
sudo ln -s /home/ABC/abmouse /home/ABC/Desktop
(you will be asked for the password, enter it)
8) Now open up a terminal window (System - terminal)
type cat > normouse
#!/bin/sh
./xkbset m
./xkbset exp =m
xmodmap .pndXmodmapnb
[Ctrl-d] <--- Dont type this actual press Ctrl-d
9) in the terminal window, type
chmod 777 normouse
10) in the terminal window type (Remember - replace ABC with your username) - This creates the symbolic link
sudo ln -s /home/ABC/normouse /home/ABC/Desktop
(you will be asked for the password, enter it)
and thats it !!!!
Your system will always start with normal AB functionality, but the two icons (symbolic links) allow you to switch function "on-the-fly"
Wicked! I find it 100000000000000000000% better with AB as mouse buttons, but as with all things its a personal preference!
(Lastly forgive my code/method/commands - any suggestions welcome - I am after all a n00b and proud of it!)
Next step is to PND it