Easy done with 1 x 3PDP relay wired in series with E-stop. Here's how it works.
One NC is for the RED LED. Two NO contacts for each Output. One Output will go to GREEN LED other to Yellow LED.

When E-stop is safe Relay will turn on and contacts change state. E-stop Contact will break path to RED LED and make path to Green & Yellow Leds.
The One OUTPUT will only ever be turned on at one time depending on state of machine so the relavent led will turn on so we only need to break the paths in case of emergency. In which case the E-stop will turn relay off and create a path to power using the NC contact to turn on Red Led.

Depending on what your wanting to display ie: System Reset or program running = Green or Feedhold = Yellow will mean having a Macro pump or brain running in the background watching.

Click image for larger version. 

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