What motion detectors are you using? How is it powered? Is the only motion detector "output" a line-voltage (120V AC) socket that presently powers both room lighting and the MRC power pack line-cord?
And when the motion detector no longer detects activity, 1 minute later it simultaneously removes AC line-voltage from the lights and the MRC power pack?
If you open up the handheld controller it looks like there MAY be a circuit board the size of the controller itself. In other words the throttle "rheostat" and the other controls and connectors might be soldered directly to a circuit board. This would make it a bit more difficult to just snip/splice a wire to insert a relay. Obviously you'll know as soon as you open it up - a photo would be nice just to satisfy my curiosity too.
Let me understand where you're going with two motion detectors. So if the "original" detector time-out is 1 minute, you'd have the 2nd detector time-out in say 50 seconds. The 2nd detector output would control a TBD relay that sets the throttle to 0 speed (while the power pack is still powered). The engine slows to a stop and then the power pack itself turns OFF 10 seconds later.
What is your thinking about what can be powered in the standby mode when the room is dark and train is stopped? That is clearly there is some minimal (a few Watts) power required by the motion detector(s). Is it acceptable to have the MRC power pack always powered but at zero-throttle when in standby mode? I can imagine alternative methods that use only 1 motion detector but in general these require electronics to be powered in the standby mode.
Finally, are you averse to changing the motion detector? Depending on how your present detector works (my questions above) there might be motion detectors that make the required timing/sequencing a bit easier.