I'd like to provide an update for anyone who might have a similar problem.
I was able to work with a team of software/control engineers at Fanuc and we found out that the positioner software that I was originally instructed to install was the wrong positioner from the robot library. There are two options in the robot library on a controlled start for a 1 Axis 500kg positioner. H875 and H887, both are listed as 1 Axis Positioners 500kg but the H887 has an iD at the end of the name. I'm unsure of the difference between the two but this did fix the issues I was having and after the 2nd motion group initialization was complete both the robot and positioner worked and I was able to master both of them.