I would simply change you WASD hotkeys to
1. remove the ~ (I hate sorn's script it is full of bad AHK practices)
2. add a * where the ~ used to be (i.e. before the WASD - *w:: *a:: *s:: *d:

This will pass throught he key modifiers then bind shift+wasd to your clones movement keys

alternatively if you don't pass wasd

create 8 hotkeys +w:: +w UP:: +a:: +a UP:: +s:: +s UP:: +d:: +d UP::
on the +w:: controlsend {shift down}{w down}
on the +w UP controlsend {w UP}{shift up}

you might want to check this against the VERY helpful help that comes with AHK as this is from memory and it has been a while since I used AHK for wow... I bought Keyclone and have never regretted it.