This is the stuff Widjet does to himself after he gets out of the mental institution. Though each part has a reason behind it.
 
The wings actually happen right after, in his twisted mind he believes he should have wings, he’s supposed to be an Alicorn, he believes himself to be some sort of god of technology. Even though he isn’t, thanks to the experiment his body still has the capacity to control the wings naturally. Attaching them to himself is a rather traumatizing experience since they bolt to the ribs of his upper back and connect to his nervous system. It’s also rather traumatizing to Pinkie Pie, since she gets to watch, at this point he’s abducted her, though really she’s going along with him, since you can’t abduct Pinkie Pie unless SHE wants you too. He plans to use Pinkie Pie to lure Twilight in so he can kill her, since he believes she tried to kill him, and caused the spell that transformed him to go wrong.
 
The eye comes after, as does that tiny scar at either end of the socket. Shining Armor and a pegasus guard show up to rescue Pinkie and it goes off the rails almost immediately. Widjet nearly removes one of Shining’s eyes with a wing, and the guard thinks he actually did, so he decides it should be eye for an eye. Widjet barely escapes, and later replaces his eye with the electronic one.
 
Throughout this whole section Twilight is completely unaware of him and his plans, Celestia tried to bury the entire thing by locking him up and erasing everyone’s memories. She even tries to erase his, and Pinkie Pie’s, but neither of them seem to respond to the spell. It’s only when Pinkie Pie tells Shining everything that Twilight eventually finds out, and it causes quite a conflict between her and Celestia.