Taking all rolling stock of the RR is a good start. Next, I would look at all the track switches, especially at the point movement and in the frog area. Next I would disconnect the power supply/commmand station and check with the ohm meter. If still a short, I'd divide the layout in half by pulling a couple rail joiners and putting a break in the bus wires. (A good reason to keep some blocks, even with DCC). Hopefully, only one side will show a short. Keep dividing to conquer.
If that doesn't work, get a few fire extiinguishers and a car battery. Hook the battery up in place of your power supply/command station. Look for smoke as whatever is shorting melts or bursts into flame. Disconnect the battery and put out the fire.
Ok, maybe don't do the last one. That sounds like a really bad idea.
Good luck