I'm pretty sure this gear (RED CIRCLE IN PIC) has an irregularity in it, (tooth/teeth displaced) and this is what you hear as the two gears are accelerated and decelerated. Hence the need to check the clearance around 360 degrees of the mating gear sets. However, placing a dial indicator on the transmission shaft is the first and best choice to asses what to do next. If it has run out, how much does it have and does it still meet spec? If RUUNOUT meets spec and you have a new gear on it, that really points the finger at the cranks drive gear. It needs inspected closely.
Its not a pleasant sound and changed drastically with the clutch gear replacement. Replacement of that alone changed the noise so much that IMO indicates it was the relationship of those two gears making the noise. Plus its the MOST LIKELY to be struck and ingest clutch debris. That's why I raise the question, "what to do with it now"??
One option may be to live with it. However this comes with huge risk that it could knock a tooth free and lock up. THIS COULD KILL YOU! A used crank is one option. Then you just have to match bearings. Something to think about.
Again, sorry. Very sorry...