DD was tested at 4 months - scratch test. So yes they can check infants for allergies. DD is also on alimentum by the way. Some babies can not even tolerate alimentum and need something broken down even further (like Elecare or Neocate) -- but by the way.
I can not comment on the nipple size -- we used size 1 for so long.. only changed to size 2 a couple of months ago. I would say try holding him more upright so he could have more control. When nursing DD & DS i had such a fast let down that they were chocking and gagging during nursing sessions. I used to have to lean back so that they could have more control over the flow -- i think the same rules apply... meaning get him more upright so he could have more control of the flow as he drinks.
Good luck... i'm so sorry cause i know all this is just so hard.