Usually, there are a few ways of narrowing down what the drivers are doing.

1. Exit LinuxCNC and Power off the board (stop-sign)
2. Check the lead-screws can be manually rotated by hand, and take a moment to lightly oil the screws with a few drops of sulfur-free (its corrosive) and detergent-free (some automotive solvents damage some alloys) oil prior to use. I just use a non-synthetic 100% additive-free 2-cycle motorcycle-oil dropper for the Taig. Note, If your machine used something like a synthetic white grease or odd looking powder, than one should always avoid mixing lubes (avoid skin/eye contact as some lubes are toxic). Remember, combining lubes chemistries can also damage the sliding surfaces with random surface galling and marring.
3. Power up the board using the green check icon
4. After powering up the board, try to lightly manually rotate the lead-screws again to check if the motors can be rotated by hand. They should hold their position rather strongly with the CNC firmware active, as this prevents loss of position during various changes in the software interfaces. If these screws can be easily moved while steppers are on, than it could mean :
   1. the motor wiring could be incorrect (there are several types of stepper motors, a photo posted with the chromium-browser in the internet menu may help me understand the setup better)
   2. current set too high for motor type, so output drivers over-heated and shut-off (will generate a high-pitched whine, and then turn off axis after a few seconds)
   3. output driver current adjusted while ON, wiring change and or no motor present while testing can fry part of a module chip's output section
   4. Current limit setting on output modules Potentiometer set too low (note your motors rated per field limit, as the driver can deliver almost 2A per winding with a heat-sink)
   5. Motor was designed to run at much higher drive voltages. Rare to see this these days, but some old equipment ran over 34v per field on some steppers to get them to move faster
5. Start the linuxCNC taig profile
6. Click the upper left button in LinuxCNC to unlock interface
7. Click the other upper left button in LinuxCNC to activate interface
8. Select an axis, an jog +1mm...  If the LinuxCNC e-stop-input is  or home-switches are active jog motions may be blocked
9. If you hear a low frequency buzzing sound while trying to jog a move, than it could mean:
   1. The kinematics of your platform need lower acceleration limits (heavier machines must move very gradually to overcome inertia)
   2. the motor winding can limit how fast one can pulse them at 12v, so the step speed limits will need tuned to ensure the output torque is not lost

=)

The GPIO are directly mapped into the HAL, and should respond accordingly unless there was a mistake in the firmware snap I pushed.

I wouldn't have seen this, as end stops are disabled on my taig (mostly fixture referenced work), but all end-stop pins should be internally biased and de-bounced with a cap.

I trying to integrate ROS right now (been a few evenings... ;-) ), but I will also have a look tomorrow to see if I missed something with the generic github version.

email me if you lost the documentation, schematics, and spreadsheet pin mapping.

edit: I just recalled we may have left  the linuxCNC inverted logic-flag on so the axis switches that are not connected don't prevent the machine from being jogged.

edit 2: Also check if the PCB routed uart jumpers are removed before running the USB serial link.  The pi uart PCB TX/RX lines can interfere with the USB TX/RX in the Arduino if both connected.