On the old F40 I’m in the process of turning into a cabbage (it’s a 10+ year old Bachman or Life Like) the flasher (which looks to be an LED to me) was directly connected to the engine or trucks to light up. When the engine blew (quite a long time ago) all of the wires were disconnected, my question is if the LED would work if I just connected the two wires emerging from the powered truck with the wires coming from the LED? If it didn’t work, what might work; I have tried a D-size battery that failed to get any light. Since the engine isn’t necessary I can remove it, so a LED power source can be rather large.
Here’s a picture of the areas in question: 
I really dont have any experince with the bachmann F40PH, but i would geuss that the LEDs were originaly wired to a circuit that would cause them to flash. in order to light them you need some sort of power regulator to control the voltage from the tracks that gose to the LEDs. if you still have the orignal circuit board it should not be too hard to re hook up, but with out it, theres a bit more work to do. I’ve made flashing beacon light circuits with a 555 timer, and im sure you could use one to make a circuit for the strobes on the top of the amtrak unit.
On another note, we have a cabbagage that runs on the surfliner out here, and the strobes on it no longer function. I talked to the engineers the first day it was in servace out here and they were really disapointed that the strobes didnt work. I dunno if that holds true for all cabbagages or not. Good luck with it.
~matt