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Thanks for the advice. Removing the files and uninstalling bootstrapper stopped it from booting into clockwork while retaining my root. For one reason or another, the update still fails using rootkeeper. One of my friends who knows a lot more about roots than I do is out of town right now. But, my phone is still working so I think I am probably better off stopping while I'm ahead and waiting until he gets back and letting him mess with it. I did the easy stuff, as much of it as I know anyway... making sure all apps are defrosted, then using ota rootkeeper. Oh well. Thanks again for your help!
You can just do the 602 sbf then root with the d3 one click root and without doing anything more grab rootkeeper and update to 621. If the 605 update shows up first you can still remain rooted by using rootkeeper going from 602 to 605 then just use rootkeeper again going from 605 to 621