M.K.
I talked to my pedi about this today since my son has a bunch of shots coming up at his 1yr appt. He said that Hep A isn't required in schools because it's not really a risk after 2yrs - this is MA but I would guess NH is the same. Hep B is required in MA (probably in NH) so you would have to fill out some sort of conscientious objector form possibly - your pedi should be able to help.
I'm not giving my kids Hep A because (according to my pedi) the only way you typically see it in the US is in a daycare situation where they are changing diaper after diaper and one kid has it. My kids aren't in daycare, so it seemed like a non-issue. I gave my kids the chickenpox vaccine because as a kid one of my sisters nearly went blind after getting chickenpox - but I know this is a very rare occurrence. Hep B I gave because my pedi was very pro it (we spent an hour discussing the issue). I agree with you though that I don't really see the necessity...
I think MMR, DTap and Polio are the most important shots to get. I lived in the UK for a while, and I remember there was a wave of students who hadn't gotten the MMR shot (because of the later discounted-by-most autism-MMR study that it sounds like you are familiar with). A bunch of them missed a lot of school because they got mumps, a couple that I knew of had pretty severe cases.
You don't mention the rotavirus, but I've been told it's a non-issue if you're kids aren't in daycare or if you're breastfeeding. Apparently breastmilk kind of counteracts the vaccine too?
My dad had to work overseas when I was a kid and for us to come along his work required that we get just about every vaccine on the planet (rabies, lyme's disease malaria, yellow fever, you name it and I've been vaccinated for it). There were ten of us and no problems, so that probably influences my vaccine stance...
Good luck figuring out what to do...