Could you explain a little more about your logic? The idea of using the same 50VDC pulses to covert to steady state DC is not something you want to atempt, There must be some kind of originating signal that turns on the shaker motor, you would want to tap THAT, and use a seperate power supply for your lights/beacons and motors.
As much details about the schematic of the machine you're talking about would help, if you don't know yourself it's difficult to provide help for such a complex electrical/mechanical scenario like that without having first hand knowledge of how the machine is actually constructed. All the tips you're going to get from the information you've provided so far are gonna get you rough guesses at best.