Kerry did well in many very anti-gay counties. The most anti-gay county in Kentucky - Magoffin - went for Kerry. The most anti-gay county in Virginia - Buchanan - also went for Kerry. Both have since moved far to the right.
I'm trying to figure out South Dakota. Apparently their anti-gay amendment was extremely restrictive and plenty of Bush-McCain-Romney- Trump voters voted against it. But it also doesn't resemble the 2016 map or PVI. TDAS, what's your take on this?
Well, it was a particularly restrictive amendment. Still surprising that it was so close. There was some correlation between votes against it and current Democratic support. The counties it failed most in were Shannon (now Oglala Lakota) and Clay (home of USD in Vermillion).
One explanation for overlap would be that in typically more more-conservative Western part of South Dakota, where the amendment had somewhat less support, they are also more libertarian than East of the Missouri (the failed abortion ban on the ballot that same year did worse in the West too).
Also, while the reservations mostly voted against the amendment, it was not overwhelming compared to how they typically vote Democratic. Opposition to gay marriage among Native American Democrats is not uncommon. After all, they are minorities.