After checking under the layout multiple times to make sure only red feeders were attached to the red bus line, and black feeders to the black bus line, I then printed out my wiring circuit and made sure that I didn't use a red wire where a black one was needed. No wires appeared to be crossed. Perhaps the Atlas crossing I installed should have had gaps cut? I looked online for help and found nothing to suggest I did it wrong. All out of options, there was nothing left to do but cut each feeder (about 20 total) where it joined the bus wire and then start from scratch with new bus wires.
Some of the switches I bought used required me to install jumper wires to connect the inner point rails. The factory bends their jumpers to sit low, but I just used a piece of code 83 nickel silver rail soldered directly to the bottoms of the rails and they were flush with the tops of the ties. I assumed it wouldn't be a problem because they would be hidden with paint and ballast. But... the center black rail had shifted a little and made contact. Barely any contact. But just enough to short out the layout. Using a hammer and a block of wood I gently tapped the black rail back in place then superglued its spikes to keep it from shifting again. I also added a small piece of stripwood in the gap to further prevent any trouble. Problem solved.

