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Steve,
You don't say what kind of boat you have. Perhaps someone has advice for removing the tank and taking it to a shop. Several years ago I had doubts about my original aluminium tank in my Tartan 30 (side galley), and removing it and taking it to a shop for cleaning and pressure testing did a lot to ease my anxieties. Yes, it meant taking apart a lot of joiner work but the tank came out in one piece.
Short of that, I don't think circulating fuel is going to do much to clean the tank. You'll get the fuel clean but the tank will still be a source of trouble. To clean the tank in place, you're going to have to pump it out then get in there with a pressure washer - likely with a hot water base alkali solution. Chemical tank ships do this sort of thing routinely.
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