I.G.
Fever and swelling/pain at the injection site are fairly common side effects. I had to get many of my childhood shots refreshed a few years ago (rather than getting titers drawn) and man - I felt terrible and my arm hurt for a week!
Also reactions usually increase with subsequent shots, because the body is recognizing the viruses and having a stronger immune reaction - that why you give shots in the first place, to trigger that immune reaction and teach the body to respond to the disease.
Now that said, you should speak to your doctor about your child's reaction. We also vaccinate on an alternate schedule and split shots (we never do more than one at a time)and I simply told our pediatrician that that was our plan and there was no further discussion or issues about that from her side.
If you wish to receive one or two shots at a time and no combination vaccines, you have to demand that your pediatrician orders them for you. If they will not do that, I would change doctors. We are talking about your child's health and you DO have a say in this! You have done your research, you have made a decision, now make your voice heard and insist that your medical decisions are respected by your physician.
We need to start being our own educated medical advocates and stop relinquishing all of our rights AND responsibilities when we go to the doctors office.
Good luck!