Just my thoughts but I'd put all those ready tracks and it's loop on a separate switches(One per track) . There are 2 reasons for this. First passenger cars and cabooses/cabeese lights drain a lot of power and drain it unnecessarily when they're just sitting. The second reason is that the smoke units in these engines run weather you've got them shut down or not and you can fry the element if you let them run dry and there they sit drawing even more power.
I said this in an earlier post. Always try to use White, Green and Black as your grounds around your layouts You can call them commons if you prefer that term.
That way when problems like this occur you can easily see if you've got a wire reversed because if it's not any of the above colors you'll know that wire is hot.
Your only recorse now is to take the track apart in sections and start checking it with an ohm meter. MAKE SURE IT"S NOT STILL CONNECTED TO THE TRANSFORMER did I say that loud enough.Not because you may turn it on but because the windings in the transformer may give you a wrong reading.
Good Luck and keep pluggin at it you'll get it and we'll help all we can
David
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