With the USB drive in UD1. To install software you have to power on the controller while holding F1 and F5. Then you select all software install.
If you then restore an AoA backup you should be good again.
If you have pulse mismatch then set mastering done = true in the system variables, then in the master/cal menu press reset PCA, and press calibrate.
If you installed options with a PAC you may need to redo that and then auto update.