I'm pretty sure the Haynes manual explains how to flush the cooling system. However you decide to do it, I'd advise against having the engine running during the flush. The cylinders must be completely submergeged in coolant when it's running to prevent creating dangerous hot spots. With coolant draining out and refilling from the header, and the likelyhood of air bubbles forming, you can't be sure that will be the case.
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