Damaged flywheels and flexplates have been known to produce noise similar to a rod knock however as posted above other facts that you have posted point to more than one issue so be aware of that fact. Also measuring with your ‘eyes’ is not going to be accurate enough for engine clearances I would suggest at the very least getting some plastigauge and checking the actual bearing clearances instead of assuming they’re good, now would be a great time to do a repair if one was required.
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