M.K.
I recommend the book, "What Your Doctor Might Not Tell You About Children's Vaccinations," by Stephanie Cave. The AAP would have us believe that vaccinations are necessary and completely safe... but there is evidence that this is not the case! Another good book on working with/despite your pediatrician, and touches on vaccines is "Raising a Healthy Child in Spite of Your Doctor," by Robert Mendehlson, MD. An older book on the subject is "A Shot in the Dark," but I do'nt know the author... it's probably on amazon.com.
If you choose to continue with your son's vaccinations, you have the right to have them done on a schedule that will be easier on his body. You can delay them until he's a year or two old, or you can split them up, so that he's only getting one shot every few weeks or months. You can also opt not to vaccinate at all anymore, or choose to selectively vaccinate (only certain shots). You might have a hard time finding a pediatrician to go along with these wishes, but they do exist! I'm sure there are moms who can give you a recommendation for a good ped who does not require vax on schedule. I can give you a couple in Charlotte or Sarasota County, if that's where you live. If you have trouble finding one, you can pm me and I can probably get you the information you need. :)
If you choose not to vax, you can obtain a religious exemption prior to enrolling him in daycare or public school. If you choose to homeschool, you will not need the religious exemption.
I wish you well... the main thing is to be informed, so start reading! There are also websites with information, but of course it tends to biased one way or another.