I have had low back (left side) pain for four months.  I have had my kidneys checked, have had an MRI, CAT scan with dye, x-rays, etc.  Everything has come back normal.  The aching is worse in the morning and keeps me from falling back to sleep.  Sitting makes it worse.  I have noticed that the pain goes out to my hip.  I have also had blood work and was told my RA factor was elevated.  I have no other pain anywhere else.  My back does not hurt when I bend over, run, etc.  Meds (muscle relaxers, etc.) do not work on the pain.  I have been to PT and to a Chiropractor.  Nothing helps.  No one seems to know what the issue is but I wake up with this every day.  One thing that is strange is that by night it is usually gone.
Here it's good that your MRI as well blood report is normal, and you do not have pain while walking running etc. Now for treatment for back pain, I suggest you to take physiotherapy treatment like ultrasound and IT along with postural correction advice for sitting and sleeping position. Also, you need to take suggestion from physiotherapist for spinal strengthening and mobilizing along with stretching exercises. Besides use hot pack and cold pack at your back painful area to relax soft tissues as well reduce inflammation from soft tissues.  For RA positive patient it is common that early morning they have pain in spine and joints for this I suggest do more over of spinal mobilization exercises. This will give you good relief. Also get your bed checked properly with physio and if needed change it for better one. You can also do some more things like following anti-inflammatory diet in your food habits too. I am sure if you follow all above things you will starts feeling better soon. Take care.