It really doesn’t sound like a short so much as it sounds like the pickups simply aren’t touching the rails. If it was a short you’d likely be tripping your circuit breaker on the transformer which I don’t recall seeing as a symptom. I’d give the pickups a good look while it’s on a section of track and ensure they’re even touching the rail before you dig into more involved troubleshooting. What Chuck mentioned will probably be your best solution.
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