RAMPS 1.4 Stepper's not getting a good signal
Turns out there were multiple faulty stepper drivers, if the one stepper driver was plugged in, it would operate, but would draw too much current from the pins on the Arduino causing all the other drivers to receive weak signals.

This is why swapping them around still only worked on the X-axis, if it was only one driver, I would have figured it out.

So if you get a very weak signal on the stepper driver step pin, even when it's pulled out, it's probably because of one of the other stepper drivers shorting the whole rail.