In Sept. 2001 I was admitted to ER with shortness of breath. At that time my 02 Sat was 63.
After two years of oxygen and prednisone 50mg. for nine months, and cyclophosphamide for nine months I am doing better, but am having terrific pain in my muscles and joints.

Yes, prednisone will do that to you.

Terribly sorry, but it's one of the gentlest immunosuppressants out there. Most of the rest are chemotherapy drugs.

My husband had by-pass surgery on Nov. 11,he was told he should be released in 5 to 7 days,finally came home on Nov. 28th.In that time he had fluid on the lungs, slight pneumonia, heart went out of rhythm, then his incision on his arm got infected. He was having problems with a cough and shortness of breath. We told the visiting nurse and she called the Dr. who then said to use Robitussin. We tried that, but the cough still persisted and the shortness got much worse. Finally the Dr. had my husband come to the office after getting an X-Ray, and suggested he go to the Pulmonary Dr. We did that immediately, and my husband's Blood Oxygen was 74%. He was put in the hospital immediately. This was on the 23rd of Dec. the 24th they took a CT scan, stopped the Cordarone (after me complaining of the side effects) and said he needed a Lung Biopsy. The biopsy showed he has Interstitial Fibrosis. That was another side effect of Cordarone. To this day, my husband, who is 56yrs old, said if I (wife) didn't come get him on New Year's Eve and take him out of the hospital, that he felt they were trying to kill him. He just came home from the Dr's, and now he needs a lung transplant. I just can't believe all this can happen so sudden.
Did anyone have similiar problems like these? I just don't know what to expect next.

The implication (they're not sure) is that interstitial fibrosis is an immunological response. Some people get it just from nobody-knows-what. It's unfortunate. Your case is typical, however.