I am in the process of studying for a large Japanese Language test (JLPT N1) for which I need to learn a large amount of characters and vocabulary (2000+ characters, 10,000+ vocabulary). I've been using the spaced-repetition flashcard program Anki, which is absolutely phenomenal in my opinion. I've also been using a couple other flashcard programs (KanjiBox is great, and Obenkyou on my tablet). I also keep a notebook of similar looking characters so I can learn to tell them apart, which I review now and then.
Then it occurred to me that I may be turning the spaced repetition algorithm on it's head by reviewing so many facts out of "order"! I can definitely say that I've been learning these facts, but is there any evidence to say that I would be better off by sticking to just my Anki flashcards? I want to say that the more often I can review the better, but I can't say with authority.
In the end, I will still be seeing these characters and vocabulary "out of order" as I am also studying reading comprehension/reading Japanese newspaper articles, and there is no way to avoid seeing characters that I am studying.