Welcome to our forum loopie89! Yeah, it's tough for you and your docs to diagnose illnesses not related to autoimmune. I think that over the years I've become more aware of my body and it's reactions. Lots of Lupies have a low fever every day. I never have a fever unless I'm very ill and even then it can take a day or two to spike.
If I have a head cold along with coughing up a small amount crud from my lungs (sputum) I don't worry about it, but if I have a persistent cough I go to my internist. If I have a chest cold I become more concerned. If my chest starts to rattle when I breathe (I call it my death rattle) I go straight to the ER, even if I'm not running a fever.
I don't think there's any way of knowing if your immunosuppressive drugs will increase your risk of your cold becoming worse. I've been taking Cellcept (a strong immunosuppressant) for 3-4 years. Yes, I have excellent hand hygiene, generally stay away from crowds, wear face masks when appropriate, and certainly stay away from anyone sick, but I currently have a mild cold. I had two teeth pulled this month (thank you Sjogren's) which caused me to flare so along with the Cellcept I just started a prednisone dose pack which starts at 60 mg of prednisone.
You shouldn't be too scared to ask your docs questions. That's why you hired them.
Just a thought: you say the prednisone isn't helping much, but without your pain shoots through the roof so it might be helping more than you think it is. Keep us posted loopie89. Love, Butterflake