Thank you, I'll try this out and see how it works, I'm guessing that I also need to fix the other tool changes as well.
(Update) it's still stopping in the same place, I'm not sure if I did it wrong or if its something else.
(T2 D=0.125 CR=0.0625 - ZMIN=-0.015 - ball end mill)
(T4 D=0.1875 CR=0 - ZMIN=-0.35 - flat end mill)
(T5 D=0.25 CR=0.125 - ZMIN=-0.0491 - ball end mill)
N0 G90
N1 G17
N3 G0 Z0
N4 T4 M6
N6 S5000 M3
N7 G54
N9 G0 X0.1255 Y0.7255