Hi there and thank you for the question. I am a Registered Nurse and will be happy to help you today.
Sometimes cardiac issues can present as shoulder pain and shortness of breath. I don't know if anyone had done a EKG on you since this started but might be a good idea.
Another thought is that gallbladder issues can cause what is called 'referred pain' -pain that goes to the shoulder(s). An ultrasound of the abdomen would be able to rule this out.
Other than these two possibilities, your viral infection may be slow to resolve because your immune system has been weakened by taking the 2 rounds of steroids. It may take a little longer for you to feel better than usual if this is the case.
To help boost your immune system, make sure you are staying well rested and well hydrated and eating a well balanced meal.
You can start taking a multi-vitamin everyday and try to get in a little exercise as well. Trying walking very short distances at a time (as long as your shortness of breath is not bothering you too much) and this will help your endurance to help you complete your everyday chores.
If your shortness of breath doesn't improve, you may need a pulmonary function test to determine if you are able to exchange enough air/oxygen like you should be able to. The indigestion could be a whole separate issue.
The above mentioned are my thoughts for you to consider and possibly take to your Dr....reply back if you need more info or further details and I'll be happy to help.