Just recently bought a 2008 beta rev 250, the kickstart jammed, seemed to have fixed that issue now a whirring noise coming from flywheel magneto? And suggestions what this could be? Are there bearings in the magneto?

Make sure that noise is not just your fan.  The bearings behind the magneto are your crankshaft bearings, it won't be that or she wouldn't run.  If it runs good, keep searching for something simple.  

The noise is worse under acceleration. Would that still be the fan?

The fan speeds up when the engine does, just give the fan blades a spin with your finger and if it doesn't make the noise that's not it.  

 

Its just the plastic cover rubbing on the flywheel. Take it off and re-center. Nothing is really wrong.

Noise is still there with the plastic cover off. Ill check the fan tomorrow 

Grab the flywheel and check for movement. It could need main bearings.

There is slight movement in the flywheel.

Definitely not the fan. Must be engine or gearbox