SOLVED:

The Windy Spirit: [GHOST]
Violet was the Windy Ghost, living in and around the old Orphange and scaring the tourists for fun. She finally communicated with the Orphans, including her brother, before officially joining them as one of the Group, though she is unknown to all but Elliot (who sensed her presence) Michelle (who sees her when she's around) and Indy (who communicates with her when in his Astral Projection form).

The Howling Spirit: [SKINCHANGER]
The old man with the ability to change into a dog. He's now been identified as the old man who once lived alongside the Ghost Witch, hundreds of years before the current day. He appears to protect those she's "Touched" with his pack of mutts, though how they threaten her has yet to be identified.

The Hunched Creature: [GHOST WITCH]
Formerly a young woman who was turned into a witch thanks to prolonged exposure to another Ghost Witch, she then used her powers to control her brother and make him murder their entire tribe, family included. All in the name of revenge. At some point she turned to dark magics, and so when she died, became the Ghost Witch which now haunts the Orphans. Why she suddenly appeared and destroyed the Orphanage is still a mystery.

The Mystery of the Rest Stop: [GHOST]
The Ghost of someone possibly killed by Donovan remained in the Rest Stop, its body hidden in the walls of one of Donovan's upper rooms, possibly why he wouldn't let any of the "Special" children up there. Once freed, it left the Rest Stop, and appeared to finally be at peace.

The Mystery of New Hope: [GHOST WITCH'S APPRENTICES]
The Apprentices of the Ghost Witch have apparently been murdering many of those who have connections to the Orphanage. Be it via Coco's "Suicides" or Donovan's "Control" abilities, they have murdered an unknown number of former wards, employees, and even people who have trespassed on the property since the incident. Nobody is safe from their wrath, though why they do it is still a mystery.

The Mystery of the Black Eyes: [COCO]
Coco's power (as well as Donovan's) appears to be the reason behind the "Black Eyes". They apparently represent any sort of "Controlling" or "Possession" powers, as the users and victims of these powers all have eyes which are black as night.

The Mystery of the Orphans: [TOUCHED BY A DEMON]
Thanks to their exposure to the Ghost Witch all those years ago, and their prolonged exposure to her, other spirits, ghosts, and the people who now work for the Ghost Witch, the children's powers have EXPLODED into the open, revealing their nature and their origin thanks to the Ghost Witch's Apprentices.

UNSOLVED:

The Mystery of the Chapel: [UNKNOWN]
The Chapel was the first place anyone felt something “unnatural” happening. The candles blow out from time to time without the assistance of a breeze, a mysterious shadow of some figure can be seen in the dark from time to time, and the priest doesn’t seem to be completely devoid of information when it comes to the occurrences around town.

The Mystery of the Last Suicide: [UNKNOWN]
The last suicide to rock New Hope brought Kevin into the mix. Not only was the victim interested in the Orphanage, but he had gathered information from the local citizens, cleaned some of the desecrated shrines, and seems to have even found a few adoption records from the Orphanage, though these should have been locked up. He was the owner of the “Book of Eyes” and since the book was taken by Kevin, is the last person to have died thanks to the “Curse.”

The Mystery in the Mirror: [UNKNOWN]
Broken mirrors have been found in multiple suicide and murder cases in and around New Hope over the last ten years. Nobody knows why it happens, although after the Compound Massacre, Nicole swears she saw something move in the room’s large chest mirror, which had been destroyed by unknown means.

NEW:

The Mystery of the Apprentices: [UNKNOWN]
There exist a group of individuals who apparently have been taught by the Ghost Witch herself. How they came about their powers is unclear, but it appears they grow stronger as she does. What the link is between these individuals and the Orphans is unclear besides the Ghost Witch, though they obviously received their powers in some other way. Known members of the Apprentices include Coco, Jene(Deceased), Lana(Deceased), Adrian, Donovan, Zoe, and an unknown younger male.

The Mystery of the Feeding: [UNKNOWN]
It appears that the Ghost Witch has been feeding on the bodies and souls of the Orphans for some time. Why only certain people have been taken and fed to her, however, is a mystery. It seems that some are free to be killed by her followers, such as Edwin and Beau, while others like Elliot, Trent, and Avery are necessary for her "diet." Known "Delicacies" of the Ghost Witch which have been either eaten or directly targeted by her or her minions include Avery (deceased/eaten), Melody (deceased/eaten), Elliot, Trent, and Michelle.

The Mystery of the Spirits: [UNKNOWN]
There are apparently numerous spirits in the surrounding areas, and a Spirit was what killed the Ghost Witch who gave rise to the current one plaguing the wards, so now some are seeking information on where and how to find one, and how to get it to kill this monster. Information appears to be very hard to come by, however.