So I'm fairly certain I overmanipulated my hive today, but I'd like to ask everyones' opinion on the right course of action. I've made it through several years of beekeeping but not very successful about getting honey, but I'm improving and last year while I didn't get any honey, I was able to build some drawn supers (the bees ate the honey while I was away).

So last week I had 2 supers with nectar present above my broodnest of a body and shallow, the bees had 2 superceudure cells going (one right below the "pollen box" as Walt Wright says) and I thought everything was going great so I added a box of foundation between the nest and the supers so there would be warmth and they could start drawing out more comb for this year. Well the rain came and the temps dropped tremendously over the weekend, and today I inspect and the 2 supers aren't being guarded much at all, there is no drawn comb, and the upper shallow of the brood nest is backfilled. They basically all clustered in the low temps and then the foundation made them forget they had supers up there!
So I freaked and decided I needed to do 2 things: Get the bees back in contact with the supers so I took out the box of foundation, and I quickly made a 4 frame nuc to open up the broodnest in the hopes that they won't swarm. I would add more drawn comb above the brood nest so my queen can keep laying but I ran out!
So questions are as follows:
1) Did I go overboard by building a nuc? If so, can I put the frames back in on Friday if I remove the emergency queen cells?
2) Can a supercedure cell turn swarm cell? Is there a behavior or cluster characteristic that will tell you which it is?
3) When is it appropriate to place foundation on top of the cluster?

Many thanks to the wisdom of the internet for your answers.