In getting ready, there have been some major setbacks. First, I accidentally applied 12V to the 5V bus and literally melted the microcontroller chips. Miraculously, that was the only damage to the Arduino's and I was able to easily switch the chips outs since they were in sockets. The motor shield, however, was not so lucky.
I ended up replacing both the L293 chips with some pin compatible SN754410s I had on hand, and the 74HC595N chip. I had to cut the chip legs with a dremel, desolder them, and then put in sockets so it wont be so hard if I do this again.
In doing some rewiring to avoid a re-occurrence of the chip cookout, I cause a meltdown of a different sort. I accidentally reversed the polarity of the 12V supply to turnout switching circuits. That supplied continuous current to the coils, resulting in failure in short order. I'm lucky I didn't start a fire. It wouldn't be the first sawmill to burn at Dawson Station (two mills burned down at the site before Ralph Hull built the current one).
The lessons learned were many, but primarily:
It is hard to idiot proof something when you are the idiot.