The cylinder would have been painted, but not the head. I'd also recommend leaving the oil pan bare if it is an aluminum one. That'll keep your oil temp a bit lower.
I guess I'd clean and paint the cylinder. The paint is going to burn off and it'll eventually rust again. Bare iron would be best for conducting heat, but it will rust. I doubt the rust is any better at heat transfer than paint, so you might as well keep it from rusting away.
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