Hope the back heals quickly.
How heavy did you start the new lift? I tend to start any new lift with really easy weights.
Did you start with a rep max? Every time Wendler has two main lifts using the 5/3/1 progression, one of the lifts is "required reps only".
Everything is individual; for me, I'd treat the Cleans as an added assistance lift. So, I'd either drop one of the one's I was already doing (GMs in this case) or limit it for a while. Throwing an extra 6 sets into a workout is a pretty big change to get used to and it may take a while. I think I would have done like Big Swede said, start really light, treat it like a warm-up exercise, and do it before the squats and deadlifts. Then as I became accustomed to the new exercise I'd start programming it with 5/3/1 required reps only. Just my 2 cents.