As long as you get #1 at TDC, the worst that could happen is a leaky gasket or something simple that you'd have to redo, along with checking for children within earshot.
Like you said, the noise could be something else. The only other thing might be the alternator, but I'd bet on the water pump too. Besides, what you're doing needs doing anyway so all's good.
Oh, have you checked the radiator fan? Pullers, sometimes when they get worn, start to rub the fins and could slide back under acceleration. Just a thought if this doesn't solve it.
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