Newly Diagnosed

Can I start by saying that I am a planner by nature.  For my whole life, I have had short-term and long-term goals.  Having some fatigue and little bit of joint pain was nothing for me to be overly concerned about.  I am a busy young mom, who works full-time in a fast-paced job as an engineer.  But in the back of my mind was fear because my grandmother had severe RA and my mom had Lupus.  So I ask my PCP to do some screening bloodwork.  Well my ANA came back positive, so off to a rheumatologist I went.  I thought I had some autoimmune disease, but not Lupus and not RA.  Then my RF and my CCP came back positive.  My rheumatologist said I may develop RA at some point and sent me home, with an appointment to return in a month.  I think I got so scared, I caused my first flare.  I awoke in the middle of the night with my arms burning from shoulders down and my fingers looked like sausages they were so swollen.
Went back immediately to see the Rheumy where he told me I probably have RA and not to worry because today the prognosis with RA is very good.  What is his definition of very good I wonder?  He gave me a script for prednisone and plaquenil.  Only informing me that some people get a little sick to their stomach from plaquenil.  Three days in to the meds, my heart started racing and I could not stop throwing up.  Went to the ER where they told me I have bug.  Rheumy said to stop Plaquenil.  On the prednisone, I could not eat, could not sleep and was feeling like i was losing my mind.  Two days later, I coughed up some blood.  Back to the ER, where they tell me after doing a chest xray that I likely tore something being sick. 
Went to see my PCP because of my concerns over these side effects and not being able to eat.  My PCP said my prognosis is going to depend on how well I tolerate medicines.  So far it is not looking too good.  I am off all meds now and waiting to get back in with Rheumy next week with more blood work of course. 
I am scared to take what medicine he is probably going to recommend, but let me say I will do anything to minimize the impact of my having this disease on my husband and son.  I have to stay strong for them and be functional for them.