Awww. I'm so sorry. :-( I hope you have better luck next time. Might try to wrap their crate up as well to keep them warmer. I find that being chilled is often the start of worse things. I'm so sorry.
Is there a place that these two sweeties can see/be seen and hear/be heard by the other four now while they heal? I know it is silly, but now I'm attached to them through your story. I never do that. LOL But I am a sucker for hurt critters. So glad you had the heart to help them out.
Wow. That is tough to deal with. I would try to separate any remaining chicks that seem to be OK, and when all of the sick ones are gone, I would basically sterilize the whole area. It seems that something besides failure to thrive is the problem, and you don't want to go through this again...
Did he make it? Did you make sure to have water (with electrolytes would be awesome) and feed right near him so he didn't have to expend much energy to get to it? Poor guy! Sounds like he is a great rooster to protect his flock like that. I lost the best rooster ever to a similar scenario. I...
Also, they would need way more than 3 days before integrating them with an existing flock. There are good threads on here about how to do that... putting them next to each other so they can see/hear the other flocks but can't get to them, etc.
Melinda, are they warm enough? 95 degrees? Try adding some electrolytes to their water as well. Add some egg yolks to the feed. It is hard when you lose chicks. :-(