I use DATA-U mode for WSJT-X instead of SSB mode. Also, you can't turn off AGC in the FT-991A menus, but if you first connect to your rig to some rig control software such as Win4Yaesu or HRD (Ham Radio Deluxe) you can turn the AGC completely off which is what I did after reading the recommendation in the WSJT-X online manual. I don't know why Yaesu didn't put an off setting in the AGC menu on the radio itself.
