I never said rod knock. Although I can't imagine those bearings being in that great of shape after running straight ATF through the engine. They are likely scored at a minimum, shortened life span at best.
What we've been talking about for a few pages now is piston slap. We already know it's not the flexplate. You found nothing wrong with it other than oblong/worn holes and that doesn't cause a noise.
Windage tray? Maybe but I doubt it. We already know the piston mishap with this engine, having some in backwards and one in the correct way, so that alone is a red flag to most of us. Someone dropped the ball there whenever it had been messed with the first time, and should have been addressed when you found it. Unfortunately I feel that thing need to come back apart completely and refreshed properly.
Yes a video would really help everyone. There are many of us here that have heard a lot of strange things with engines. Without a video we can only guess, but from descriptions you've stated up to this point, there isn't much left to guess at and it starts to narrow things down to what some of us have mentioned already. Fingers crossed it's simple, but at this point I'm thinking it's more involved.
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