In Shingeki No Kyojin, when does Eren lose 3 years of his memory?
From the manga and from the anime I don't remember Eren losing 3 years of his memory. From your timeline I think your pretty accurate, except that I would switch 3 and 4 around, as I think that Eren's dad went deeper into the wall to kill the real royal family.[Chapter 1, page 44] He killed the royal family by turning into a titan. Therefore I think it was only after he turned back to a human that he headed back to his home when the news of wall Maria fallen reach Dr. Jaeger.[[Chapter 62, page 19-24]][1] He probably then starts looking for Eren in every camp (where the survivors of wall Maria stay) there is to find Eren. As the royal family is looking for him, he needs to disappear. To do so and still fulfill his goal he injects a drug into Eren who eats his dad and gains Titan powers alongside the "coordinate".[Chapter 3, page 21 ] [[Chapter 10, page 32-35]][2]

Edit:
The only part I don't quite get is when Eren says to his dad "You've been acting weird ever since mom died"[Chapter 3, page 21]. It's the only time where it looks like Eren has seen his dad after the fall of wall Maria and before he turned into a titan, so that might be an indicator of a 3 year void in Eren's memory, even though this would be just speculation.