Jay,
I will try my best to answer some of your questions...
For starters most will tell you that trying to grow juvies in such a big tank and with other larger fish is not ideal. It seems like you are doing a good amount and size of water changes but most here will frown upon the set-up. I have never grown out such small juvies or done anything remotely close to your set-up, so I can't speak directly on it, just telling you based upon much reading and being apart of this forum...
That being said... Did you QT any of the additions as they went in? You said you started w the small pigeons then came the turq's. With small juvies such as yours, their immune systems are growing and developing and if there was an issue w those turqs, it would easily be passed over to others, especially smaller, developing fish.
By change the pads, you mean removed them and added new? Can they not be squeezed in tank water to clean and put back. Most of your beneficial bacteria is going to reside on those pads and is essential. It sounds like you learned your lesson on that front and pulled through...
As far as your concerns with the breathing and stress bars. Depending on where your tank is and the activity going on you are going to see different things. I wouldn't be too concerned about the bars and the breathing, unless it is really over the top, you could have startled them or my fish seem to breathe heavier as they eat or are chasing others...
In my experience the true indicator for not only fish but any animal is appetite and eating. Once they stop eating or show no desire or interest in food, something is up... Many discus will turn dark and try to hide or not be very social, again early signs that there is an issue. As well as the feces, white feces or anything abnormal will tell a story as well...
Hope this helps a bit...
Do you have the ability space or tanks to raise the fish in a smaller tank until they grow?