Neonatal Encephalopathy??

I was induced at 38 weeks and my son was born by a C-section.  The delivery was traumatic because my son had not dropped and he kept floating up in my uterus.  Both doctors had a difficult time getting him out.  When he was born he was having a hard time breathing b/c his lungs were not developed.  His APGAR was 6/6.  He was transferred to a Neonatal Intensive Care Unit.  On day 2 he had a seizure which was stopped with phenobarbital.  Day 3 he was intabated and given surfactant.  A CT Scan showed that his brain looked normal, an EEG was normal.  He did have a hard time taking a bottle and didn't suck very well and he was unable to maintain his body temperature.  He was released from the hospital on day 15, still not taking a bottle well and unable to maintain body temp.  Also, after delivery, his fontanels were overlapping for several weeks.  Health-wise he is fine now.  Our pediatrician ordered an MRI and it came back normal.  He hasn't had a seizure since the one in the hospital.  However, he does have craniosynostosis and will have surgery in a month.  Our neurologist told us that he believed the craniosystosis was from the trauma during delivery.  He is behind on his milestones.  He is 4 months old and still can't hold his head up completely on his own.  The neonatalogists put on discharge report that he had neonatal encephalopathy however they told us that they weren't really sure what caused his problems.  Could too much pressure during the delivery have injured his brain?  If so, would that have shown up as in either the EEG, MRI, or CT Scan?  Or if he did have neonatal encephalopathy, what will be the outcome for his future?