Got this all working. The new features in RRF3 are awesome.
daemon.g
if sensors.inputs[4].value == true && fans[1].actualValue == 1.0 ;Checks if the Fan is showing a stuck rotor alarm and also checks if the fan should be spinning
G4 S1 ;Buffer in case the fan took a second to spin up
if sensors.inputs[4].value == true && fans[1].actualValue == 1.0 ;Second check to see the fan is still in alarm
echo "OH CRAP WE STUCK" ;Console message that can be checked on the PanelDue to see what happened
M106 P1 S0 H-1 ;Turns off Thermostatic control on the fan so it doesnt try and turn back on
M112 ;Emergency Shutdown