I'm an idiot - who built the device in part 1?
My conjecture is that it was Mr. C with the drug money that he had been earning: the purpose of the glass box was to capture Cooper at a dimensional portal. It's not clear how/why BOB would know of this location, but it appeared to be an elaborate trap that was foiled. If you recall, Cooper did enter the box, but too soon. When Cooper was in the box appeared to be the time when the kid left the room, but Cooper was gone when he returned. When the experiment/mother did spawn in the box he wasn't there to be gored, but the 2 kids were instead. The other likely person was Jeffries, but he seemed to have it in for Mr. C not Cooper. Plus, like Kyle mentioned above, there is a pic of Mr. C in the room.