What Could Cause Restless, Eratic Sleep In A Child?

My baby had whooping cough at three weeks old and it would wake her during sleep, she would turn red. Since being hosptialized for 3 days with antibiotics the whooping cough subsided. However her sleep is erractic. During naps she only can sleep 40 min and awakes abruptly. But what concerns the family is that she tosses and turn every 2 to 5 minutes in her sleep starting at 5 30 am for hours not fully waking, but appears in distress. Mom will wake her after hours of tossing and turning. She used to do this at night also but she now sleeps soundly from 11 pm until 4 am for her feed. The pediatrican is concerned. we tried acid reflux meds, but didnt make a difference. why can she only sleep for 40 min naps, but more importantly why does she toss and turn every 2 minuetes? Plus my pregnancy I was under a lot of stress due to a new job, and felt anxiety and depression. Could the prental care and whooping cough cause this sleep problem and will it go away?