If you do not load an encoder in hal, those pins can be used as IO.
All pins on 7i92 can be used as gpio, no matter what mesaflash says for stepgen, pwm, encoder, etc, just not loading those functions will leave pins as IO.
In this case, you are limited by BOB, but if you need an encoder, load just one in hal, then you have 2 pins on that port as inputs and all 5 on the other port.
Thanks a bunch! Yes, so everything is what I'd suspected I'd have to do. I'm going through the Hal file now and making sure everything is pointing where it should be. Thanks for these replies, helps with my sanity check!