The attached video shows how my CT2 idle hangs up for a bit at around 2500 rpm and then settles down to a proper idle. I just installed new Yamaha crank seals and o-ring in it and a brand new clutch. Was hoping the crank seals would’ve sorted out the hanging idle because it sure did on my DT175C a few months ago. I have checked for air leaks with my simpleton method of spraying starting fluid around the likely areas. (Head joint, cylinder base, carb mount) The RPMs did not vary at all during that process.

Any suggestions? Maybe I should just carry on and have fun with it.

The new clutch works awesome. I paid a lot for Yamaha frictions as opposed to using the aftermarket stuff. So I’m sure glad they work so well. 

As for the top end noise……. All my bikes sound like this video. My phone exaggerates the top end noise tenfold.

That's a sign of leaness at idle . Turn the Air Screw in 1/4 or 1/2 turn , which should settle it .
If at that point , the Air Screw is less than 1 1/4 turns out from lightly seated , you might need the next size larger  Pilot Jet .
 

It's definitely too lean at idle & just above where it's hanging for a bit. Thing is "why". First I'd richen the idle mixture but if you are limited by screw adjustment & if that doesn't help then I'd look at removing the pilot jet & poke something through it, bit of wire brush strand etc. But also poke the pilot hole straight up but importantly the progression hole on an angle. Actualy i think its the other eay around & straight up is progression but anyway they link up to the pilot jet. Think I would go at least a notch richer on the needle too, clip down. Otherwise are there any air leaks like base gasket which would be obvious if that bad. Broken or compromised reed valve petal. Broken piston skirt on the exhaust side. OK I'm getting stupid now so leave it at that but sure sounds piston noisy although clutches rattles on those if the 'big' rubber ring isn't installed between drum & gear. Causes chatter rattle at idle but as you say your phone accentuates any noise. Sorry im no real help just throwing random thoughts out there.