Dear Colin,
A similar question has been answered in the following forum topic: Gain Scheduling.
With regards to the AeroDyn settings, the big difference from what is given in Appendix B.1 is that the controller gains were derived with StallMod = STEADY; that is, with the Beddoes-Leishman dynamic-stall model disabled.
Please note that Appendix B.1 shows the primary AeroDyn input file for AeroDyn v12.60i, which is a version that was never formally realized. However, the results should be very similar to what is currently set-up in the AeroDyn input files for the NREL 5-MW turbine in the FAST v8 release. Also note that the controller gains were derived from an AeroDyn solution that employed a frozen wake assumption during linearization, as discussed in the forum topic linked above.
Best regards,