"New Englanders don't like switchbacks, I am convinced." Yes, Ben, you're correct! Straight up and over. :)
I also did the 100 Mile last summer, averaging about 20 miles a day, in trail runners. As far as terrain goes, it's nowhere near as gnarly as some parts of New England...Even with trail runners, I MUCH prefer stream crossing barefoot (with poles and a light pack, I don't think the danger of slipping is any greater than in shoes). My shoes stay dry, and my feet get rinsed off, which helps prevent blisters.
Foot conditioning, I have learned, is a very individual thing. I spend a lot of my time barefoot when I'm at home, which includes walking around on bare rock, gravel, etc. I've never worried about wearing heavily padded shoes at work, even back when I was on my feet all day in hard-floored warehouses/grocery stores/etc. So I'm probably not a good person to speak to issues of foot pain. I think adapting your feet to lighter/more minimal shoes can take years, and for some people it just never clicks. Don't beat yourself up over it, just find what's most comfortable.
I love leather hiking boots for their durability; the arguments for them are as compelling as the arguments against (but this is backpacking LIGHT, so, you know...). Boots often run a little wider than trail runners, so it might be worth seeking out trail runners with an extra-wide last (something with a boxy-looking toe like Altra's offerings, perhaps) and see if that helps.
Lastly, ditch those Drymax socks. Synthetic can be a killer, especially if it has some kind of treatment, whether antimicrobial or hydrophobic. Treated, synthetic socks make my feet blister--and I don't have blister-prone feet. Go with lightweight merino socks, like Darn Tough's lightweight crew. They're way more comfortable when damp and offer superior climate control if your feet sweat much. I switched entirely to wool socks years ago and never looked back. Darn Tough may seem pricey, but they last just about forever.