I have been using an FTdX-3000 for 4 years and run it almost exclusively in Data Mode. with a number of data software programs. I have the menu settings configured to run always in DATA MODE 1 (OTHER) rather than using the PSK mode for Menu Item 067.
Attached is an image showing the settings that I am using. Also note the frequency settings that are configured in Menu Items 068, 069, and 070. These settings have always worked for me with all of the data mode programs that I am using WSJT-X, Fldigi, VARA, Winlink, MMSSTV, and including VarAC.
I hope this is helpful.
73, Rick VE3ORY