We vaccinated our children, before I had even heard about "not" doing it. Thankfully, our children never have had any side effects that were lasting. I thank God for that. Going forward, with all the info out there now, it is scary to think about the possibilities of what exists within the vaccines that could react with our body.
A middle of the road approach would be to space them out at the very least, and certainly not combined together, and only get ones that prevent life threatening diseases.
I'm like you PO... I try to "cook from scratch" as well.
ND - I would suggest reading the Nourishing Traditions book by Sally Fallon. It is probably the best cookbook you can get with amazing recipes, all using real food ingredients. You can find it on amazon
here and also there is a book by the same author on Baby and Child care found
here