The (false) Paleblood Hunters won't wake up simultaneously, no, though given that most of them probably received the treatment to become Hunters at about the same time, their time of awakening will probably be reasonably close to one another. Since you're the first one with a character in that scene to post, you kind of have control of how much time your character has before the next one wakes up (within reason... think minutes, not hours).
I don't think a Hunter waking from metamorphosis would be in pain, no. By the time he was ready to wake up the transformation would be complete, and there shouldn't be any reason for it.
And no, the (false) Paleblood Hunters waking up won't be buried in Messengers; the Messengers only do that to the dead. They don't even crawl on them at all. Rather, he will just wake up to being surrounded by them, with them sitting at the edge of his cot and on the floor, staring at him.