A lot of things such as autism or ADD are more visible in group care because part of the syndrome is the child's inability to cope with confusion which doesn't happen one on one. With the ear issues the noise levels could be deafening to him so anytime a voice is raised above a whisper he freaks out. His behaviour is still out of sync for a child that is 2 1/2 and something we would also be complaining about so his speech levels do not account for this part of his behaviour. Unfortunately even medical staff get caught up in blaming everything on one thing instead of looking for more than one cause. The behaviour needs to be addressed separately but has probably been ignored because of the amount of time and effort that has been put into the speech and ear issues.
Not sure trying to put a 3 year old in a hyper state in a playpen was a good idea. A sectioned off time out/cool down spot using the play yard would be one option that doesn't involve lifting - more just dragging. Some like this actually need to be restrained to calm them down. Get behind and cross the arms in front and bring them to their sides holding them so they can't move them. When the arms stop flailing, start to pull child down to the floor so they are sitting in front of you and your body is more or less enveloping them giving them security. Sounds bad I know but sometimes the only way to help them gain composure because self soothing is still beyond them and will need to be taught over time - not during a tantrum.