I'm fixing to do a restoration on my survivor 71' Roadrunner 383/4sp/AC car built June 10, 1971. While taking notes of what parts are what color and looking for chalk marks, I noticed my water pump, housing, and thermostat are painted black while the rest of the motor is the typical hemi orange.

Most cars I've seen have the water pump and other parts painted the same as the motor. Any idea if this is correct or would be a good idea to keep them black?

Since they painted the engine as a whole, I'd go with it all one color!
There are threads here on correct engines, take a look at what has been accepted as normal.