Hello @Ed1Flying ,
if you see the AP/red lights turning on at all,
I think that the AFC_Bridge was set up correctly. If some of the buttons are not lighting up as you expect them to, the only solution I am aware of is doctoring with the config file from AFC_Bridge. The config file should contain MSFS variables that trigger the individual lights. Currently, I can live with the inconsistent lights and if you wanted to correct them, maybe you could either try yourself manually, try to find appropriate the config file online for specific aircrafts, or ask honeycomb support, if they could improve the AFC_Bridge.
The AFC_Bridge should only affect the lights of your peripheral, but not actual AP behavior in MSFS.