For those that may be wondering what has happened to me, after trying absolutely everything I could think of with the copy of Marin given here, I gave up and decided to start with a fresh copy of Marlin, copying all the variables I could find from the one here. It is working 100% better than it was, but I still don't have a functional printer.
I finally solved the thermocouple problem. On issue I had, was figuring out which way to hook it up. The thermocouples in the description look nothing like the one in any of the images, so eventually, I hooked it up to an Arduino. Lo and behold, I had the wires switched. Then, it took me a moment to figure out pin assignments. I can't make heads or tails of those circuit diagrams and how they relate to pin numbering in Marlin.
Thermocouples work. All of the motors work. Heaters work, although I need to find different software to control extruder 2. MatterControl still assumes I have only one heater. It heats really fast though. Holy cow!
There seems to be an issue with the controller thinking it is at home when it turn on. The head won't move past where it is when it starts. I don't think it's an endstop issue, but this is next on my list of bugs to solve.
Most importantly though, I still can't get VIKI to function. As far as I can tell, its all hooked up correctly. Without VIKI, the printer is pretty worthless. I need to print from the SD card.