I avoid posting here as a general rule, but I might be the only person with the answer because I asked a former Insomniac employee personally. When I mentioned Dr. Shemp to Oliver Wade, he said that the name is indeed a reference to the Three Stooges and to any trouble they had while making the game. I think he said the line that was passed around the office when they were having trouble was something like "Looks like you pulled a Shemp" (it's been around two years since I had this conversation with him, so my memory is rusty).