It sounds like you have been through a very frightful experience.
There are a couple of things that come to mind.
Growing is so much more than physically becoming bigger. Children go through emotional growth and awareness expansion. Your little one may simply be more aware of things that he was oblivious to in the past. Because he is just aware of it, he may be startled by it and needs your reassurance.
Another possibility, and I do not say this to be alarmistic because it is unlikely, but he may have a nerve impingement. Your call to the pediatrician is good, they can do a neurological check to make sure everything checks out ok. Nerve pain can occur speratically and is quite intense while it is happening, then it goes away. I know of a young girl who had trigeminal (it is a cranial nerve) neuropathy that was misdiagnoses for several years. It is considered highly unusual in the young. Medication improved it once it was properly diagnosed.
Regardless of the cause of your child's "freak outs", your calm, attentive reasurrances are a good way to help your child. Keep open to any other ways he may be trying to communicate with you. Hang in there! Be persistant with the pediatrician. Let us know what happens.