After failing to make the motor run properly, after trying quite a few different firmwares, I came across a testing firmware for RAMPS, that will wiggle all the motors, pulse all the heater outputs, and read the thermistor inputs continually.
After fixing the weak connection on the motor connector (usual suspect) I found that all the drivers worked fine, except the X. All were tested using the same Pololu, so the actual driver can be excused.
This set me on a path that almost cost me the new board… The 10k and 100k resistors were reversed, and in swapping them I unfortunately lifted one of the pads. I had to solder a 10k Resistor on solder-side to fix it up again. This did not solve the problem though.
With the program running, I measured the frequency of pulses going to each of the pins. It turns out that all the inputs were fine, except the STEP line. Well, no STEP, no step. Makes sense. I found a dry joint in the header going towards the Arduino, and realized that it was where I tacked the header on to straighten it before soldering. After a quick re-flow RAMPS is wiggleling on all its axis!
Now I have no excuse but to start assembling the mechanics of the bot.