Quick update...the rooster seems to be all well. As soon as I got the junk out of his eye, it cleared up and was completely normal the next day. The Swedish Flower Hen, however, still has the eye issue. She is still alive and actually doing very well, just the eye infection that will not go away.
Now, for the bad news...I alerted the breeder that I got my birds from about my issues and encouraged them to get their birds tested. They did and just got the results back. They found that one of their pens was positive for mycoplasma (MG) and it was the pen some of my birds were in. So, that pretty much diagnoses my birds with mycoplasma as well I would say. That said, I have thought it over long and hard and talked it over with my wife and daughter. We are NOT going to de-populate and start over. I have read a LOT about myco and believe we can deal with it. Sure, it means no birds in or out and our birds will be more likely to get sick. That is fine, I can deal with that. I just can't see killing all of these creatures just because they are most likely carrying something. Oh, and I not some pansy yuppy afraid to kill when needed. I hunt and kill numerous deer each year to put food on the table. Besides, from the research I have done, it is claimed that around 80% of backyard flocks are infected with myco already anyway. I could kill them all and start over, just to have it show up again. Just not willing to do that.
I spoke to the breeder I got my birds from and she has 7 two month old chicks from the infected pen that she has not killed yet. She knows she needs to kill them, she just has not had the heart to do so yet. She said I can have them no cost if I don't plan to just kill them. I may just go rescue them and add them to my flock.