One tip is to not present the previous vaccinations done. I'm not saying to lie and say they weren't done, but don't present the vaccinations done previously and an exemption letter, that can cause some issues. Just present the exemption letter.
If it comes up that there were previous vaccinations, then you explain that you had a religious awakening in the interceding time. You are of course legally allowed to change your beliefs.
However, just so you know, you can't selectively vaccinate from now on. You can't present an exemption letter and then say "oh, but we'll vaccinate for just ______." Its all or nothing.
We are in a similar situation; DD was vaxed up to 9 months and we're also in MA. I haven't presented her exemption letter yet so I don't know how it will go. From what I've read here, it seems like most often, it goes without a hitch, no big deal. A few times there are some raised eyebrows and challenges - if so, answer as few questions as possible (unless you actually ARE JW, for example, don't tell them what religion you are and just say that you are constitutionally protected). You don't have to be any particular religion to ask for an exemption. Also note that you need to be religiously opposed to the PRACTICE of vaccination.
DH is a little worried about how this will go over but since we're willing to homeschool, I figure it's no big deal. Either the exemption goes fine, or we decide whether to homeschool or vaccinate. Personally I don't want to vaccinate, but just leaving all the options open.