Just to provide some closure for those who read this in the future. I noticed Pncconf has a checkbox to invert the direction. This changed the sign of the SCALE value in the ini file. So, you could just manually edit your ini file and add a negative sign before the scale value for each axis.
Alternately, I read you can use ".invert_output" to change the sign of the direction parameter in the hal file. I didn't try that method, but other threads here discuss it.
I also setup the charge pump. Using Pncconf, I enabled the 5th stepgen on the 7i76e and selected Charge Pump from the drop down menu. To connect it to the G540 I ran a wire from the G540 (DB25 - pin 16) to the 7i76e (TB3 - Pin 3). That is the STEP4+ signal. I tied in TB3 - pin 1 with the other stepgen grounds (TB2 - pins 1,7,13,19).