Sorry bit of a typo there :
What I am meaning is the start of the manual says Y Step is 16 and Y Dir is 3 and the screen print on the board seems to suggest that is right however further on in the manual it shows 3 as Step and 16 as Dir.
What I would do is disable all axis in Mach except X then try pin 2 and 3, 2 and 3, 2 and 5 etc etc. Unfortunately there are a lot of different combinations for you to try.
You should be able to test by jogging with the keyboard keys rather than trying to command moves.
A few other things you can try, you need to set the steps per unit correctly, for that you will need to know what microstepping you have the drives set to and if there is any gearing between motor and screw and also what pitch the screws are. Also try with 10 set for step and dir pulse boxes in Motor tuning.
Another thing, do you have the Breakout board powered?
Hood