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Hard to keep it clean if you do it first. In your case I would do all the bodywork, then when it's truly ready to paint, I'd drop the engine out the bottom, prep and paint under the hood, reinstall the engine from the bottom and paint the exterior.

Sheldon

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I did mine first and the guy who did it told me it was difficult(not impossible) to smoothly transition where you stopped on the engine bay and started on rest. But it also didn't hold up too well when I put the engine back in. Not the paints fault at all.