Has Miko been dead the entire time...
No, because others including those that aren't "spiritually sensitive" have interacted with her. That being said Miko's probably been exposed to ghosts to a point that she's got that "leftover residue" deep down in her skeleton-bones.
Also, kind of cool they did the "
Oculus" thing where what they saw wasn't what they were getting. He just about killed his girlfriend. A hard lesson for both of them to learn.