So minor bolts count towards the next headshot, but do they apply it? If so, do they land before or after the actual auto-attack (just in general)
Headshots only apply on the attacked target, because the headshot is technically an on-attack, not an on-hit. This also goes for things like Lulu's Pix, Staatic Shiv, Sheen, Sivir's bouncing blade, and similar effects.
Where things like frost shot, toxic darts, the headshot stacking, and stuff are all on-hit, therefore ruunan's applies them. But it's not really a good item to get because it puts you out of position.