Starlight, as ever, I would recommend Richard Halvorsen's book (you've probably read it, as I think I mentioned it to you when you had dd)
there is quite a lot of info re: the vaccine schedule, and the risk/benefits etc.
as you know, I know exactly what you mean wrt the parallel universe, and getting decent info on any of this can be very difficult.
I will be facing this again too, over the summer (so far our decision will be as for dd2, but then we are coming form a slightly different angle from you, as you know, with a lot of gut issues in the family, and in dd1 and dd2).
there are few options other than the recommended ones for babies. some are available for older children, but this does railroad parents of newborns into "our way or no vaccines at all" which is not helpful.
We will be visiting Halvorsen for a consultation after dc3 arrives - to get an opinion o n what to do with dd2, as well as up to date info on his thoughts re: dc3.