At least as far as I’ve seen, the only time the screen shakes during the E > J parts is if you put a onyumi when it’s looking for kunyomi or vice versa. I think I would recommend the double check script as this might provide what you are looking for. It enables you to retype the answer if you mispelled something and got the question wrong.
EDIT: I’m embarassed to say I didn’t read your whole post and see that the reading you put should actually be correct as well. I’ll leave the recommendation though in case anyone else would like to check it out