Hi Gary
I just emailed you , but with the guys said above is absolutely correct! This engine has more electronics, and wiring then pretty much any engine Lionel has produced. It’s actually more complicated then the VL Big Boy. Unfortunately trying to locate this short is like trying to find a needle in a haystack. My guess would be its a pinched wire or a protruding solder joint from a circuit board shorting out.
I haven’t serviced a challenger in quite a while , but in the pictures here , I think there’s suppose to be an insulator over the board ( PCB Regulator) i took pictures of. I think there might be exposed solder joints on this board. Also there’s a wire with heat shrink Im pointing to. Make sure that’s not squashed.