Newly diagnosed, looking for answers

I haven't been feeling well for several months now. My GP ordered tests and found I was ANA positive and assumed I had lupus based on my symptoms. I went to a rheumatologist last week and after running labs he said I have Hashimoto's disease, not lupus. My symptoms were/are extreme fatigue, weight gain, muscle fatigue & weakness, joint pain & swelling, sensitivity to light. I am an avid runner & triathlete who is now struggling to be able to run more than 3 miles when only a few months ago I was running 10+ several days a week. My rheumy had put me on prednisone and it made me feel better but not 100%. I was able to get out of bed, go to work and workout on a good day but not like I used to. There are still days that working for 12 hours makes me too tired to function after work which is not me. He told me today to stop taking the prednisone since that shouldn't help with Hashimoto's and told me to take aleve twice a day.
My question to anyone who may know is if I only had Hashimoto's would the steroid have worked? I did feel better once I was on it I just still had muscle weakness and some joint swelling. I also have bruises on my legs that I have had for 3 months. I'm nervous that stopping the steroid will down me again.
I'm starting to get very worried that Ill never feel good enough to run distance or workout like I used to since I'm still struggling and I'm supposed to be training for a marathon in October. There are days I can't get out of bed from the pain & fatigue. Is this normal with this disease? Will only the thyroid supplement meds work to get me feeling better in time? If so, about how long does it take?

Would the thyroid cause such severe pain and weakness in my joints & muscles?
For my labs my TPO is 160 (reference interval 0-34) and my C-Reactive protein, Quant is 13.7 (reference interval 0.0-4.9).

I'm thinking the prednisone would help you feel better if you also had adrenal fatigue. Perhaps your cortisol levels are low.