It sounds like your turtle could be a little box turtle; as their shell and skin are brownish orange. They typically grow to a maximum of 8" depending on what type of North American Box Turtle they are. You can find a lot of information online or in the library.
It is impossible to say. Turtles shells can actually vary quite a bit based on their enviroment and their diet. He could be a Eastern Soft Shell turtle, or he could have a vitamin deficency.
