5 is wrong.
3 seems wrong, but may be okay, just uncommon.
"Passed away" and "gone" are both nicer ways of saying "dead." However, "gone" has a literal meaning. If you say "Now that Mary is gone, who will lead the project" you may cause concern among your listeners -- they may wonder if Mary is dead. Howeve, they are more likely to understand that Mary is no longer an employee.
Do you understand the difference between present perfect and simple past?
She passed away.
She has passed away.
This is no different from "She made dinner" and "She has made dinner" grammatically. Do you understand the difference?
Student or Learner