Factory reset is not focusing

There is no such thing as a factory reset with Nikon cameras. The greatest reset (restore costume settings) you can get is in the Custom settings menu.
The first line in that menu is Reset custom settings. If you use that, it will reset more settings, that with the green button restore. It won't involve or switch back switches you have put from AF to M, on the camera body or on the lens.
If your camera does not show and ERR on the Control panel, it is not likely your lans has any problem.
Refer to the manual, to see how you should put all the switches on the camera if you are not sure you did something wrong.