7i98 and 5abobx3 firmware

Sounds like you have the x axis connected to stepgen 1

I thought that also but y step is P1 pin6. I checked the hal and checked the bit file and the hal reads x axis is joint 0, y is1, z is 2 etc.
is that indeed referance to the particular numerical value of the axis?
The bit seems to reflects this too. I will double check though. Still very new to this so thank you for your patience.

I thought that also but y step is P1 pin6.

That would make sense if you mapped

X = joint0 --> stepgen1
Y = joint 1 --> stepgen2

i would agree but it doesnt explain why the dir pins are what they are
x dir = p14
y dir = p16
z dir = p17

again i found these by trial and error. i found step first by pressing jog and jumping the stepper drive step pin to the bob output pins.
then secured the step wire and jumpered the dir signal checking each pin and jogging back and forward looking for the motor reversing direction.

and i have realised that x is set as stepgen1 in hal so 4 is technically correct however the breakout board normally uses pin2
if i can understand how the direction pins are going where they are i can always look into writing a new bit file to better suit my needs

I think I would renumber the stepgens
starting with 0 first so

X=joint0=stepgen0
Y=joint1=stepgen1
Z=joint2=stepgen2