First let me say thanks so much for the hard work you and others are doing to figure this out!
I'm not sure if this helps or is already known, but the AI Upscaled Gore optional mod from Improvements in Blood causes trains to spawn empty for me (aside from conductor). I noticed you mentioned using an upscaled gore mod - is it a different one from the one I mentioned?
Anyways, I'm eagerly awaiting the results of your WhyEm's DLC texture edit!