Reassign Breakout Board pins in PathPilot?

How do I change the input and output pins in PathPilot? 
- I'm using the PCNC 440 setup with 7i92 Mesa card.
- I bought a driver board that doesn't match the 440's pin-out.

Not my first PathPilot build, I've installed it on 2 machines using standard BOB's. They run quite well. 

If you can prevent PathPilot from re-writing the firmware
you could use firmware with the correct pinout for your BOB

Note that the GPIO pins would not change with different
firmware, but things like the step/dir, encoder or PWM pins
can be moved anywhere.

Meaning edit in the Mesa firmware?
It looks like I can edit it on the 440 HAL file. I just don't understand Linux terms and commands well enough to know how to reassign io db25 pins.
Any advice to help me figure out how?

PCW will write the firmware for you and post it here. It doesn't have anything to do with your knowledge of linux.

You have to tell him what pinout you need. Since you mentioned DB25 I assume you have a 7i92TM. Look at the manual and find the IO number for the pins you want to do what, make a list and post it here.

Pins are GPIO by default so nothing changes with those, you assign them as input/output in HAL. Encoders, pwmgens, stepgens are modules, a stepgen has 2 pins for example, so list what pins of the connector you need as step and direction.

Thanks! So if I'm understanding you right, I can swap step and dir pins in HAL, without firmware changes?
Or all changes require firmware changes to match?

What actual breakout board do you have?
There is likely existing firmware that has the correct pinout