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Scraping and prodding is a good idea if you have the engine torn down far enough to do it. Otherwise, I agree with Tim and say fill it with "Evaporust" (Or maybe "Rust-911" which is a concentrate and a bit cheaper). Let it sit a day or two, and then hit it again. It did the job on a '51 Mercury engine I picked up.
It will turn black when you drain it, so you will know it's working.