Other things to possibly know..

I tried adding some oil (seemed a little low) no change to the noise.

im running premix, the oil injection is disconnected and was that way when I got the bike.

Good video thanks, Ok, does it at think 5 then 6 seconds briefly plus more later in the vid. Better get into the clutch side & check the center nut & while ya there slide the plates out ^ grab the center to see if the shaft rocks like a problem with the bearing the far end--which is just in from where you say it sounds on the left. Also feel the backlash in the cush rubbers the basket buffer against internaly. Even if they are stuffed with a lot of play back n forth the heavy rubber ring would probably stop the noise, not the play as such but dampen it to get by. Number 9 in the link looks like a needle bearing. Hope its not that. Another thought is feel the crank bearings on both sides as noise can sound from one place but but can fool us sometimes & i'm an expert fool. Just grab each end of the crank via the auto advance on the left & crank nut on the right. if its as bad as it sound then play will be obvious. Can hear piston rattle but that's the least of worries & videos make things sound worse than they are.

www.partzilla.com/catalog/yamaha/motorcy.../dt125b/transmission

piston slap?

Thanks I’ll check those items out. Is the piston slap separate or could that be the primary cause of the noise? I could handle that being the case as it wasn’t warm, i can try seeing if it goes away when it gets warmed up.

the prob is the concept of opening up the case is somewhat intimidating to me and where I live (middle of nowhere) there aren’t a whole lot great options to choose from shop wise.

as an example I thought the clutch was on the left side of the engine. Wrong.

Could an extremely High oil level be causing this weird rattling sound. Im pretty sure my crank case is almost filled to the top right now and i drove it around my backyard a bit and when downshifting , holding in the clutch, it has a weird rattle noise coming from the left side. It may be the chain guard. Going to check right now ....

Post a video, that will help our resident experts in giving a proper diagnosis...  And well I'd like to hear/know what's going on too.

Not being pedantic here but why not drop the oil to the correct level then you will know.

Crankcase as in transmission i guess you mean--not crankcase as in where the crank is. I've forgotten what bike we're talking but should have a dipstick. Sometimes it's best to drain it all & start again with correct volume but don't go looking at dipstick for a while as takes time to level out right through the trans internals. Bike vertical when checking.