Following the new flow chart, Whisper gets to cloak before Dengar fires back, but would Whisper get her focus token (assuming she hit) before Dengar fires back from his ability?

Yes.

You handle all triggered effects that don't start a new attack first (in Initiative order, if both players have them). Only then can a new, separate attack get triggered.

As Quarrel said.

Whisper would shoot.

Gain focus token if she hit.

Cloak

Gain target lock from fire control systems.

Then Dengar would get his payback shot.