It sounds to me like you're tinkering overly much and not letting the bees be bees. The nonpreforming queen should be killed as well as any supercedure cells that orginated from her. Mediocrity begats more mediocrity when it comes to queens. It would have been much better to get your supercedure cells from a hive that has a queen with better brood raising characteristics.
You're objective at this point is to focus on getting each hive (nuc) into shapre to winter over--even if it means combing 2 or more into one hive. In combining, always select the queen with the best brood pattern and largest size brood nest.
Curb your impulses and concentrate on developing good quality of bees over quantity of hives.