If I had to guess, I'd go with the B12, maybe the ACV. Some people do better with a hydroxy form of sublingual B12 instead of methyl, and sometimes still it can start up chemical pathways that have been dormant for quite a while, and headaches and junk can occur.
When are you taking the ACV? I had an odd reaction to lemon juice (all alone, not as a normal ingredient in things), I think it's the acidity, it was on an empty stomach first thing in the morning. I didn't feel bad, but I did have some strangeness. Perque makes a hydroxy b12, there are some liquid B12 drops around too, I haven't ever tried them, just read about them....http://www.holisticheal.com/supplements/b12-products
If it's an issue of circulating toxins (B12 suddenly restarting your methylation and things being imbalanced for a while), consider vitamin C, as much as you can take w/o getting gastro side effects. Maybe skip the B12 for a couple days, add in the C, see if anything changes?
Those supps do seem like most of the heavy hitters, things we tend to be low in. Um, you may want to add a B-complex, the Bs tend to work together, just to prevent any subtle imbalances there. I wouldn't think that would be the cause of the things you've described though, just to help smooth the way, prevent subtle stuff later on. Thorne makes supps with real folate (half 5-mthf, half folinic acid), you can look through their offerings and see what fits (either a multi or just a b-complex).