The Yeasu FTDX3000 is a peculiar beast on HF digital, breaking some of the “norms” that you would follow with most other radios - specifically some shift settings.
When selecting your data mode, be sure you are on the correct sideband. When you see [data] displayed on the screen, a long press of the mode button will switch between LSB and USB. For packet you'll often want to be on LSB.
This radio has a built in audio interface so a single USB cable between the radio and computer will take care of both audio interfacing and control functions.