I would too look up the bearings first as Twin-Shocker mentioned, just take off the ignition cover then try to push and pull flywheel forward and backward, sidewards and up and down.
If there is some play when pushing or pulling the rotor this is still OK, if there is play when you push / pull sideways or up or down then the main bearings has to be exchanged.
While you have the ignition cover off you can test the crank seals, start the engine and then spray some WD 40 or brake cleaner between rotor and engine case and rotor, when the idling will change than you have an air leak.
Just to mention:
The Yamahas have some weird sound expecially the 250cc engines not really healthy compared to other engines, the 125 normally don't produces so much ratteling noise.
Please check you intake manifold for cracks too, also check the reeds that are in the intake, there might be some issues too like corroded plates, ...