You should speak with his doctor about the vaccines and determine if he should continue them (is short term discomfort worth the risk of not getting the vaccines). Also, make sure you stay in the office for at least half an hour after he gets a shot to make sure he's not going to suddenly have a severe reaction.

Yes

I feel crummy for three days after any vaccines shot I get (even as an adult), but I am not allergic to the ingredients in the vaccines.

I'm allergic to milk and never had any issues with vaccines. Maybe it is just how he reacts to a vaccination in general. My little guy isn't his normal self for a few days after shots either.