I have had what sounds like this same bug. They get it, get better, get worse, and sadly about 2 out of 5 of mine have not made it. After awhile, no drug works, the ones that have made it, I have given Enterolyte High energy(HE), and milkreplacer, and stopped the drugs, and isolated from the others. The bad part with pneumonia, is it damages their lungs, and with some calves, weakens them so bad, that they can't recover no matter what, and then are more susceptible to other diseases.
I know Nuflor is not meant for repeated doses, 1 time 3cc's, and then another within 24 hrs, another 3 cc's, or 6cc's all at once, with maybe another 6cc's in a weeks time, but no more than that. For me, I find Excenel works the best for alot of things in baby calves, and if they get too weak, having a vet treat them is also a good idea.
Hope this helps
Gail