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You should have diagnosed it b4 doing all that, shoulda killed each cyl. but since it still has the knock you can still do it, you may have a rod out of round.
I would have gone as far as a compression test, etc....
unfortunately, a rattle can come from a worn connecting rod bushing, which won't show with regular diagnostics... The engine would need to be dismantled, and each rod checked by measurment to determine.
The next time you're willing to pull an engine, may as well be prepared to just rebuild it.
A mild bore, new pistons/rod bushings/bearings, at the very least. From there, a top end can be swapped out a lot easier. Rattles generally come from the bottom end, where clatters come from the top end. Valves and lifters tend to clatter pretty consistently, when worn, but bottom end rattles can be inconsistent, as they might disappear under acceleration or deceleration, and may not be there at idle. Valves and lifters just clatter all the time when worn.
Probably not this, but something to be mindful of: A friend bought an old F-100 and when he went to overhaul the engine, he found it had one oversized bearing. Nothing was marked. People do strange things at times.