Outputs will not work when in E-Stop as they are all switched off. It depends what you actually want for the E-Stop signal, for example if you want the Light to be on when code is not running then you could just invert the Run signal in the Brain for that output. If you are actually wanting it to show the E-Stop then you would have to have a relay that is powered from maybe an enable output and so when powered, ie Mach not in E-Stop the Light will be on.
For the others what you want is No Operation Pass Signal option rather than a compare imediate.
Hood